awesome-genome-visualization
This is a companion website for the github repo https://github.com/cmdcolin/awesome-genome-visualization
Also check out our twitter account @awesomegenomev1
Feel free to submit PRs to add more tools
ATCC Genome Portal
https://docs.onecodex.com/en/articles/3996697-using-the-genome-browser
Interactive: true
Tags: Commercial, Microbiology
Platform: Silo
Golden Helix
https://www.goldenhelix.com/products/GenomeBrowse/
Interactive: true
Tags: Commercial
Note: Free for academic use
AA (alignment annotator)
http://www.bioinformatics.org/strap/aa
Publication: (doi link) (2014) (# citations 52)
Language: JS
Tags: MSA
Note: also see STRAP
Platform: Web
abrowse (MSA viewer)
https://github.com/ihh/abrowse
Language: JS
Tags: MSA
Github Stargazers: 11
Platform: Web
alignment.js
https://github.com/veg/alignment.js
Language: JS
Tags: MSA
Github Stargazers: 6
Platform: Web
AlignmentComparator
http://bioinfweb.info/AlignmentComparator/
Language: Java
Tags: MSA
Note: Uses http://bioinfweb.info/LibrAlign/
Github: https://github.com/bioinfweb/AlignmentComparator
Github Stargazers: 1
AlignmentViewer
Publication: (direct link) (doi link) (2020) (# citations 4)
Language: JS
Tags: MSA
Github: https://github.com/sanderlab/alignmentviewer
Github Stargazers: 24
Platform: Web
AliView
http://www.ormbunkar.se/aliview/
Publication: (doi link) (2014) (# citations 2154)
Language: Java
Tags: MSA
Github: https://github.com/AliView/AliView
Github Stargazers: 106
Platform: Desktop
BioJS/MSA
Publication: (direct link) (doi link) (2016) (# citations 144)
Language: JS
Tags: MSA
Github: https://github.com/wilzbach/msa
Github Stargazers: 167
Platform: Web
rMSA
https://github.com/mhahsler/rMSA/blob/master/vignettes/rMSA_vignette.pdf
Language: R
Tags: MSA
Note: Can automate boxshade
Github: https://github.com/mhahsler/rMSA
Github Stargazers: 8
Boxshade
https://embnet.vital-it.ch/software/BOX_form.html
Publication: (direct link) (doi link) (2000) (# citations 7)
Note: Also available as a command line tool with `apt install boxshade`. See also rMSA which can automate running boxshade from within R
Platform: Web, CLI
ESPript
http://espript.ibcp.fr/ESPript/ESPript/
Publication: (doi link) (1999) (# citations 2384)
Tags: MSA
Note: Primarily a web interface but can download a binary for linux https://espript.ibcp.fr/ESPript/ESPript/esp_faq.php
Platform: Web, CLI
JSAV
http://www.bioinf.org.uk/software/jsav
Publication: (direct link) (doi link) (2014) (# citations 14)
Language: JS
Tags: MSA
Github: https://github.com/AndrewCRMartin/JSAV
Github Stargazers: 11
Platform: Web
LogoJS
https://logojs.wenglab.org/app/gallery/
Publication: (doi link) (2020) (# citations 7)
Language: JS
Tags: Logo
Github: https://github.com/weng-lab/logojs-package
Github Stargazers: 14
Platform: Web
MSABrowser
https://thekaplanlab.github.io/
Publication: (doi link) (2021) (# citations 1)
Language: JS
Tags: MSA
Github: https://github.com/thekaplanlab/msabrowser
Github Stargazers: 29
Platform: Web
msaR
https://github.com/zachcp/msaR
Tags: MSA
Note: uses BioJS/MSA
Github Stargazers: 8
Platform: Desktop, R/htmlwidget
MView
https://www.ebi.ac.uk/Tools/msa/mview/
Publication: (doi link) (1998) (# citations 288)
Tags: MSA
Note: See also their web versions of clustal omega etc. which have similar outputs
Platform: Web, Silo
pyBoxshade
https://github.com/mdbaron42/pyBoxshade
Language: Python
Tags: MSA
Note: also see boxshade
Github Stargazers: 21
Platform: Desktop
React MSAViewer
https://github.com/plotly/react-msa-viewer
Tags: MSA
Github Stargazers: 24
Platform: Web
seqotron
https://github.com/4ment/seqotron
Publication: (doi link) (2016) (# citations 33)
Language: Objective-C
Tags: MSA
Github Stargazers: 28
Platform: Desktop
STRAP
http://www.bioinformatics.org/strap/
Publication: (doi link) (2014) (# citations 52)
Tags: MSA
Note: also see AA
Platform: Web, Applet
TeXShade
http://mirrors.ibiblio.org/CTAN/macros/latex/contrib/texshade/texshade.pdf
Publication: (doi link) (2000) (# citations 263)
Tags: MSA
Platform: Desktop
Wasabi
Publication: (doi link) (2015) (# citations 48)
Tags: MSA
Github: https://github.com/veidenberg/wasabi
Github Stargazers: 16
Platform: Web
aCNVViewer
https://github.com/FJD-CEPH/aCNViewer
Publication: (direct link) (doi link) (2017) (# citations 5)
Language: Python
Github Stargazers: 24
CNVkit
https://cnvkit.readthedocs.io/en/stable/plots.html
Publication: (direct link) (doi link) (2016) (# citations 1201)
Language: Python
Tags: CNV
Github: https://github.com/etal/cnvkit
Github Stargazers: 461
BAMScale
https://github.com/ncbi/BAMscale
Publication: (direct link) (doi link) (2020) (# citations 36)
Github Stargazers: 61
BAMSnap
https://github.com/parklab/bamsnap
Publication: (doi link) (2021) (# citations 5)
Language: Python
Tags: Static, Alignments viewer
Github Stargazers: 105
ChIA-Pipe
https://github.com/TheJacksonLaboratory/ChIA-PIPE
Publication: (direct link) (doi link) (2020) (# citations 20)
Tags: Static, Epigenomics
Github Stargazers: 26
Chimeraviz
https://github.com/stianlagstad/chimeraviz
Publication: (doi link) (2017) (# citations 22)
Language: R
Tags: Gene fusion, Circular, Linear
Github Stargazers: 34
CNView
https://github.com/RCollins13/CNView
Publication: (doi link) (2016) (# citations 10)
Language: R
Github Stargazers: 67
CNVPlot
https://github.com/dantaki/CNVplot
Publication: (doi link) (2015) (# citations 0)
Language: R
Github Stargazers: 15
CNVpytor
https://github.com/abyzovlab/CNVpytor
Publication: (doi link) (2021) (# citations 35)
Language: Python
Github Stargazers: 154
DNAPlotLib
https://github.com/VoigtLab/dnaplotlib
Publication: (doi link) (2016) (# citations 47)
Language: Python
Tags: Static, Synthetic biology
Github Stargazers: 280
FeatureViewer
https://github.com/calipho-sib/feature-viewer
Publication: (doi link)
Tags: Static, Gene structure
Github Stargazers: 103
Platform: Web
Geneviz
https://jrderuiter.github.io/geneviz/usage.html
Language: Python
Tags: Static, Gene structure
Github: https://github.com/jrderuiter/geneviz
Github Stargazers: 15
Genome STRiP
http://software.broadinstitute.org/software/genomestrip/
Publication: (doi link) (2015) (# citations 335)
Tags: Static
GenomeTools
Publication: (doi link) (2013) (# citations 325)
Language: C
Tags: Static, Gene structure
Github: https://github.com/genometools/genometools
Github Stargazers: 272
GenomeView
https://github.com/nspies/genomeview
Publication: (doi link) (2018) (# citations 2)
Language: Python
Tags: Static, SV, Alignments viewer
Github Stargazers: 138
GenomeView (java app)
https://genomeview.org/content/quick-start-guide
Publication: (doi link) (2011) (# citations 115)
Language: Java
Tags: Alignments viewer
Github: https://github.com/GenomeView/genomeview
Github Stargazers: 7
genoPlotR
http://genoplotr.r-forge.r-project.org/
Publication: (doi link) (2010) (# citations 553)
Language: R
Tags: Static, Comparative
ggbio
http://www.bioconductor.org/packages/2.11/bioc/vignettes/ggbio/inst/doc/ggbio.pdf
Publication: (direct link) (doi link) (2012) (# citations 250)
Tags: Static, Ideogram, Circular, Multi
Github: https://github.com/lawremi/ggbio
Github Stargazers: 108
GGsashimi
https://github.com/guigolab/ggsashimi
Publication: (doi link) (2018) (# citations 151)
Tags: Static
Github Stargazers: 108
GSSPlayground
https://github.com/orangeSi/GSSplayground
Language: Perl
Tags: Comparative, Static, Alignments viewer
Github Stargazers: 28
gtrellis
http://bioconductor.org/packages/devel/bioc/vignettes/gtrellis/inst/doc/gtrellis.html
Publication: (doi link) (2016) (# citations 18)
Language: R
Tags: Static, Ideogram, Quantitative, CNV
Github: https://github.com/jokergoo/gtrellis
Github Stargazers: 39
Gviz
https://bioconductor.org/packages/release/bioc/html/Gviz.html
Publication: (doi link) (2016) (# citations 653)
Language: R
Tags: Static, Alignments viewer, Quantitative, Multi
Github: https://github.com/ivanek/Gviz
Github Stargazers: 64
Hagfish
https://github.com/mfiers/hagfish/wiki/Plots
Language: Python
Github: https://github.com/mfiers/hagfish
Github Stargazers: 36
HiCPlotter
https://github.com/kcakdemir/HiCPlotter
Publication: (doi link) (2015) (# citations 157)
Language: Python
Github Stargazers: 16
JVarKit/BamToSVG
http://lindenb.github.io/jvarkit/BamToSVG.html
Publication: (doi link)
Language: Java
Tags: Static, Alignments viewer
Methplotlib
https://github.com/wdecoster/methplotlib
Publication: (doi link) (2020) (# citations 22)
Language: Python
Tags: Static, Epigenomics, Methylation
Github Stargazers: 80
Millefy
https://github.com/yuifu/millefy
Publication: (doi link) (2020) (# citations 4)
Language: R
Tags: Single cell
Github Stargazers: 25
Platform: Package
pauvre
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6991124/figure/fig-3/
Publication: (doi link) (2020) (# citations 15)
Language: Python
Tags: Static, Misc QC, Comparative
Github: https://github.com/conchoecia/pauvre
Github Stargazers: 47
Platform: CLI
PureScript genetics browser
https://github.com/chfi/purescript-genetics-browser
Language: Purescript
Tags: GWAS
Github Stargazers: 5
Platform: Web
pyGenomeTracks
https://github.com/deeptools/pyGenomeTracks
Publication: (doi link) (2020) (# citations 221)
Language: Python
Note: See also https://pypi.org/project/gtracks/ which is a separate project that is powered by pyGenomeTracks
Github Stargazers: 704
RACER
https://oliviasabik.github.io/RACERweb/articles/IntroToRACER.html
Publication: (doi link) (2018) (# citations 4)
Language: R
Github: https://github.com/oliviasabik/RACER
Github Stargazers: 16
RepViz
https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-019-4473-z
Publication: (doi link) (2019) (# citations 0)
Language: R
Tags: Static, Quantitative
Github: https://github.com/elolab/RepViz
Github Stargazers: 2
Samplot
https://github.com/ryanlayer/samplot
Publication: (doi link) (2021) (# citations 45)
Language: Python
Tags: Static, SV, Alignments viewer
Github Stargazers: 476
SashimiPlot
https://miso.readthedocs.io/en/fastmiso/sashimi.html
Publication: (doi link) (2015) (# citations 128)
Language: Python
Tags: Static, Expression, Splicing
Note: See also rmats2sashimiplot which uses MISO. MATS stands for Multivariate Analysis of Transcript Splicing
Github: https://github.com/yarden/MISO
Github Stargazers: 128
shinyChromosome
http://150.109.59.144:3838/shinyChromosome/
Publication: (direct link) (doi link) (2019) (# citations 15)
Tags: Dotplot, Linear, Ideogram
Github: https://github.com/YaoLab-Bioinfo/shinyChromosome
Github Stargazers: 41
Platform: Web
SparK
https://github.com/harbourlab/SparK
Publication: (direct link) (doi link) (2019) (# citations 35)
Language: Python
Tags: Static, Hi-C, Quantitative
Github Stargazers: 100
Sushi
https://www.bioconductor.org/packages/release/bioc/vignettes/Sushi/inst/doc/Sushi.pdf
Publication: (doi link) (2014) (# citations 171)
Language: R
Github: https://github.com/PhanstielLab/Sushi
Github Stargazers: 64
svist4get
https://link.springer.com/article/10.1186/s12859-019-2706-8
Publication: (doi link) (2019) (# citations 32)
Language: Python
Tags: Static
svviz
https://github.com/svviz/svviz
Publication: (doi link) (2015) (# citations 42)
Language: Python
Github Stargazers: 81
svviz2
https://github.com/nspies/svviz2
Publication: (doi link) (2015) (# citations 42)
Language: Python
Github Stargazers: 46
TnT
https://tnt.marlin.pub/articles/introduction
Publication: (doi link) (2016) (# citations 3)
Tags: Gene structure
Github: https://github.com/tntvis/tnt.genome
Github Stargazers: 18
Platform: Web, Interactive
trackViewer
https://bioconductor.org/packages/release/bioc/vignettes/trackViewer/inst/doc/trackViewer.html
Publication: (doi link) (2019) (# citations 130)
Language: R
Tags: Static, Lollipops, Quantitative
Github: https://github.com/jianhong/trackViewer
Github Stargazers: 53
Aequatus
https://github.com/TGAC/Aequatus
Publication: (doi link) (2018) (# citations 1)
Tags: Comparative, Deadlink
Github Stargazers: 7
Platform: Web, Silo
AliTV
https://alitvteam.github.io/AliTV/d3/AliTV.html
Publication: (doi link) (2017) (# citations 61)
Tags: Comparative
Platform: Web
Artemis comparison tool (ACT)
https://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act
Publication: (doi link) (2005) (# citations 1338)
Language: Java
Tags: Comparative
Github: https://github.com/sanger-pathogens/Artemis
Github Stargazers: 224
Platform: Desktop
Biodalliance comparative demo
http://biodalliance.org/dev/test-comparative.html
Publication: (doi link) (2011) (# citations 89)
Language: JS
Tags: Comparative
Github: https://github.com/dasmoth/dalliance
Github Stargazers: 226
Platform: Web
Chromatiblock
https://github.com/mjsull/chromatiblock
Publication: (direct link) (doi link) (2020) (# citations 1)
Language: Python
Tags: Comparative, Pangenome, Microbiology
Github Stargazers: 28
Platform: Web
CMap
Publication: (doi link) (2009) (# citations 63)
Language: Perl
Tags: Comparative
Github: https://github.com/gmod/cmap
Github Stargazers: 5
Platform: Web
CoGe
https://genomevolution.org/coge/
Publication: (doi link) (2017) (# citations 124)
Language: Perl
Tags: Comparative, Dotplot, Linear, JBrowse integration
Github: https://github.com/LyonsLab/coge
Github Stargazers: 44
Platform: Web, Silo
Comparative assembly hub / "snake track"
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296145/
Publication: (direct link) (doi link) (2014) (# citations 26)
Tags: Comparative, UCSC integration
Platform: Web
CrossBrowse
https://github.com/shenkers/CrossBrowse
Publication: (direct link) (doi link) (2018) (# citations 0)
Language: Java
Tags: Comparative
Github Stargazers: 8
Platform: Desktop
CVit
https://sourceforge.net/projects/cvit/
Publication: (doi link) (2011) (# citations 26)
Language: Perl
Tags: Comparative, Ideogram
Github: https://github.com/ekcannon/CViT
Github Stargazers: 2
Platform: Web
Cvit.js
https://github.com/LegumeFederation/cvitjs
Language: JS
Tags: Comparative, Ideogram
Github Stargazers: 10
Platform: Web
EasyFig
https://mjsull.github.io/Easyfig/
Publication: (direct link) (doi link) (2011) (# citations 2485)
Language: Python
Tags: Comparative
Github: https://github.com/mjsull/Easyfig
Github Stargazers: 84
Platform: CLI
Edinburgh-Genome-Foundry/DnaFeaturesViewer
https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer
Publication: (direct link) (doi link) (2020) (# citations 76)
Language: Python
Tags: Microbiology, Synthetic biology
Note: See also https://github.com/Edinburgh-Genome-Foundry/Caravagene
Github Stargazers: 533
Platform: Desktop
GBrowse_syn
http://gmod.org/wiki/GBrowse_syn
Publication: (doi link) (2010) (# citations 32)
Language: Perl
Tags: Comparative
Github: https://github.com/GMOD/GBrowse
Github Stargazers: 49
Platform: Web
Genome Context Viewer
https://www.legumefederation.org/gcv/phytozome_10_2/
Publication: (doi link) (2017) (# citations 24)
Language: JS, Typescript
Tags: Comparative, Gene order
Github: https://github.com/legumeinfo/gcv
Github Stargazers: 33
Platform: Web, Silo
Genome-plots-processing
https://github.com/filip-husnik/genome-plots-processing
Publication: (doi link) (2016) (# citations 208)
Language: Processing
Tags: Comparative
Github Stargazers: 1
Genomicus
https://www.genomicus.biologie.ens.fr/genomicus/
Publication: (doi link) (2021) (# citations 38)
Tags: Comparative, Ideogram, Dotplot
Platform: Web, Silo
gggenomes
https://github.com/thackl/gggenomes
Publication: (doi link) (2020) (# citations 2)
Language: R
Tags: Comparative
Github Stargazers: 533
Platform: Package
GIVE
https://zhong-lab-ucsd.github.io/GIVE_homepage/
Publication: (doi link) (2018) (# citations 15)
Language: JS
Tags: Comparative, Linear, Quantitative
Github: https://github.com/Zhong-Lab-UCSD/Genomic-Interactive-Visualization-Engine
Github Stargazers: 138
Platform: Web
mauve-viewer
https://github.com/nconrad/mauve-viewer
Language: JS
Tags: Comparative
Github Stargazers: 37
Platform: Web
MCScan (python version)
https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)
Publication: (doi link) (2015) (# citations 317)
Language: Python
Tags: Comparative, Dotplot, Linear
Github: https://github.com/tanghaibao/jcvi
Github Stargazers: 681
Platform: CLI
MCScanX
https://github.com/wyp1125/MCScanX
Publication: (doi link) (2012) (# citations 3881)
Language: Perl
Tags: Comparative, Dotplot, Circular, Linear, Ideogram
Github Stargazers: 184
Platform: CLI
mGSV (multiple genome synteny viewer)
https://github.com/kashmatic/mGSV
Publication: (doi link) (2012) (# citations 17)
Tags: Comparative, Deadlink
Github Stargazers: 5
Platform: Web, Silo
MizBee
http://www.cs.utah.edu/~miriah/mizbee/Overview.html
Publication: (direct link) (doi link) (2009) (# citations 119)
Language: Processing
Tags: Comparative
Platform: Desktop
Multiple genome viewer
http://www.informatics.jax.org/mgv/
Publication: (doi link) (2021) (# citations 2)
Tags: Comparative
Github: https://github.com/mgijax/mgv
Github Stargazers: 11
Platform: Web, Silo
OMA local synteny browser
https://omabrowser.org/oma/synteny/ADH1A_HUMAN/
Publication: (doi link) (2020) (# citations 135)
Tags: Comparative, Gene order
Platform: Web, Silo
Parasight
https://baileylab.brown.edu/parasight/galframe.html
Publication: (doi link) (2005) (# citations 739)
Language: Perl
Tags: Comparative
Note: Examples at https://ratparalogy.gs.washington.edu/
progressiveMauve viewer
http://darlinglab.org/mauve/user-guide/viewer.html
Language: Java
Tags: Comparative
Github: https://github.com/koadman/mauve
Github Stargazers: 20
Platform: Desktop
SyMap
http://www.agcol.arizona.edu/software/symap/
Publication: (doi link) (2006) (# citations 153)
Tags: Comparative, Dotplot, Linear
Platform: Desktop
Synima
https://github.com/rhysf/Synima
Publication: (doi link) (2017) (# citations 36)
Language: Perl
Tags: Comparative
Github Stargazers: 54
Platform: CLI
Synteny browser
https://github.com/TheJacksonLaboratory/syntenybrowser
Tags: Comparative
Github Stargazers: 4
Platform: Web
SynTView
http://hub18.hosting.pasteur.fr/SynTView/documentation/
Publication: (direct link) (doi link) (2013) (# citations 22)
Tags: Comparative, Dotplot, Linear, Microbiology
Platform: Desktop, Web, Flash
SynVisio
Tags: Comparative, Linear, Dotplot
Github: https://github.com/kiranbandi/synvisio
Github Stargazers: 74
Tripal MapViewer
Publication: (doi link) (2019) (# citations 4)
Tags: Comparative, Ideogram
Github: https://github.com/statonlab/tripal_map
Github Stargazers: 1
VISTA browser
http://pipeline.lbl.gov/cgi-bin/gateway2
Publication: (doi link) (2004) (# citations 1770)
Tags: Comparative
Platform: Web, Silo
XMatchView
https://www.bcgsc.ca/resources/software/xmatchview
Publication: (doi link) (2018) (# citations 3)
Language: Python
Tags: Comparative
Github: https://github.com/bcgsc/xmatchview
Github Stargazers: 35
Platform: Desktop
AGB assembly graph browser
Publication: (direct link) (doi link) (2019) (# citations 12)
Language: Python
Tags: Graph
Github: https://github.com/almiheenko/AGB
Github Stargazers: 74
Platform: Web
Bandage
https://github.com/rrwick/Bandage/
Publication: (direct link) (doi link) (2015) (# citations 1547)
Language: C++
Tags: Graph
Note: See also BandageNG https://github.com/asl/BandageNG
Github Stargazers: 553
Platform: Desktop
gfaestus
https://github.com/chfi/gfaestus
Language: Rust
Tags: Graph
Note: See demo video displaying GFF3 annotations on graph https://www.youtube.com/watch?v=A-HnKXIrJl4
Github Stargazers: 57
gGnomes.js
https://github.com/mskilab/gGnome.js
Language: JS
Tags: SV, CNV, Breakends, Graph
Github Stargazers: 26
Platform: Web
graphgenomeviewer
https://cmdcolin.github.io/graphgenomeviewer/
Language: JS
Tags: Graph
Github: https://github.com/cmdcolin/graphgenomeviewer/
Github Stargazers: 7
Platform: Web
MoMi-G
https://github.com/MoMI-G/MoMI-G
Publication: (doi link) (2019) (# citations 20)
Language: JS
Tags: Graph, Multi, Alignments viewer, Circular, SV
Github Stargazers: 81
Platform: Web
odgi draw + odgi viz + odgi inject
https://odgi.readthedocs.io/en/latest/index.html
Publication: (doi link) (2021) (# citations 14)
Language: C++
Tags: Graph
Note: Example from https://github.com/pangenome/pggb, see also gene arrow map https://odgi.readthedocs.io/en/latest/rst/tutorials/injecting_gene_arrows.html
Github: https://github.com/pangenome/odgi
Github Stargazers: 175
sequence tube map
https://github.com/vgteam/sequenceTubeMap
Publication: (doi link) (2019) (# citations 27)
Language: JS
Tags: Graph
Github Stargazers: 164
Platform: Web
Alan
https://github.com/mpdunne/alan
Language: Bash
Tags: Text based, MSA
Github Stargazers: 108
Platform: CLI
Alv
https://github.com/arvestad/alv
Publication: (doi link) (2018) (# citations 3)
Language: Python
Tags: Text based, MSA
Github Stargazers: 103
Platform: CLI
ASCIIGenome
https://github.com/dariober/ASCIIGenome
Publication: (doi link) (2017) (# citations 4)
Language: Java
Tags: Text based, Alignments viewer
Github Stargazers: 192
Platform: CLI
Bamcov
https://github.com/fbreitwieser/bamcov
Language: C
Tags: Text based, Coverage
Github Stargazers: 94
Platform: CLI
BLAST+ (reading -outfmt 0 pairwise output is the original CLI bioinformatics!)
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
Publication: (doi link) (2009) (# citations 13170)
Language: C++
Tags: Text based
Platform: CLI
plotReads
http://campuspress.yale.edu/knightlab/ruddle/plotreads/
Tags: Text based
Platform: CLI, Static
pyBamView
https://mgymrek.github.io/pybamview/
Publication: (doi link) (2014) (# citations 6)
Language: Python
Tags: Alignments viewer, Static
Note: See supplementary info for more figures, supports padded SAM/BAM which is fairly rare
Platform: CLI
Rna Alignment Viewers (Colorstock, SScolor, Ratón)
http://biowiki.org/wiki/index.php?title=Rna_Alignment_Viewers&redirect=no
Publication: (direct link) (doi link) (2008) (# citations 3)
Language: Perl
Tags: Text based
Platform: CLI
Sam2pairwise
https://github.com/mlafave/sam2pairwise
Publication: (doi link)
Language: C++
Tags: Text based
Github Stargazers: 40
Platform: CLI
Samtools depth visualization
https://twitter.com/yokofakun/status/1178686978541441025
Language: C
Tags: Text based, Coverage
Platform: CLI, GNUplot
Samtools tview
Publication: (doi link) (2009) (# citations 44600)
Language: C
Tags: Text based, Alignments viewer
Github: https://github.com/samtools/samtools
Github Stargazers: 1523
Platform: CLI
SvABA
https://github.com/walaj/svaba#alignmentstxtgz
Publication: (doi link) (2018) (# citations 272)
Tags: Text based
Github Stargazers: 222
Platform: CLI
VizAln (from HipSTR)
https://github.com/tfwillems/HipSTR
Publication: (doi link) (2017) (# citations 207)
Tags: Text based
Github Stargazers: 86
Anvio
https://peerj.com/articles/1319/
Publication: (doi link) (2015) (# citations 1330)
Language: Python
Tags: Circular
Github: https://github.com/merenlab/anvio
Github Stargazers: 396
BioCircos.js
http://bioinfo.ibp.ac.cn/biocircos/
Publication: (doi link) (2016) (# citations 111)
Language: JS
Tags: Circular
Platform: Web
Circleator
http://jonathancrabtree.github.io/Circleator/index.html
Publication: (doi link) (2014) (# citations 32)
Language: Perl
Github: https://github.com/jonathancrabtree/Circleator
Github Stargazers: 45
circlize
https://github.com/jokergoo/circlize
Publication: (doi link) (2014) (# citations 2531)
Language: R
Github Stargazers: 930
Circos
Publication: (doi link) (2009) (# citations 7933)
Language: Perl
Note: the github repo is not up to date with the latest code
Github: https://github.com/vigsterkr/circos
Github Stargazers: 67
CircosJS
https://github.com/nicgirault/circosJS
Language: JS
Tags: Circular
Github Stargazers: 499
Platform: Web
DNAPlotter
https://www.sanger.ac.uk/science/tools/dnaplotter
Publication: (doi link) (2008) (# citations 684)
Language: Java
Tags: Circular
Platform: Desktop
GenomeProjector
https://github.com/gaou/g-language/wiki
Publication: (direct link) (doi link) (2009) (# citations 32)
Language: Perl
Github: https://github.com/gaou/g-language
Github Stargazers: 1
Platform: Desktop
JupiterPlot
https://github.com/JustinChu/JupiterPlot
Publication: (doi link)
Language: Perl
Tags: Circular, Static, Comparative
Github Stargazers: 63
mummer2circos
https://github.com/metagenlab/mummer2circos
Language: Python
Tags: Static
Github Stargazers: 87
OGDRAW
https://chlorobox.mpimp-golm.mpg.de/OGDraw.html
Publication: (doi link) (2019) (# citations 1086)
Platform: Web
seqviz
https://github.com/Lattice-Automation/seqviz#viewer
Tags: Synthetic biology
Github Stargazers: 198
Platform: Web
ApE (a plasmid editor)
https://jorgensen.biology.utah.edu/wayned/ape/
Tags: Synthetic biology
Twitter: https://twitter.com/apeplasmid?lang=en
Platform: Desktop
Apollo
https://web.archive.org/web/20060927154956/http://www.fruitfly.org/annot/apollo/
Publication: (direct link) (doi link) (2002) (# citations 268)
Language: Java
Tags: Historical, Deadlink, Gene structure, Annotation, Comparative
Note: URL is an archive.org link
Platform: Desktop
Apollo aka WebApollo
https://genomearchitect.readthedocs.io/en/latest/
Publication: (doi link) (2013) (# citations 303)
Tags: Gene structure, Annotation, JBrowse integration
Github: https://github.com/gmod/apollo
Github Stargazers: 122
Platform: Web
Chromatic
https://chromatic.nci.nih.gov/
Publication: (direct link) (doi link) (2018) (# citations 4)
Language: WASM
Tags: Alignments viewer
Platform: Web
cnvCurator
http://www.acsu.buffalo.edu/~lm69/cnvCurator
Interactive: true
Publication: (direct link) (doi link) (2015) (# citations 2)
Language: Java
Tags: CNV, Annotation, Deadlink
Platform: Desktop
D3GB
Interactive: true
Publication: (doi link) (2017) (# citations 12)
Tags: Gene structure, Coverage, Variation
Note: Live link http://d3gb.usal.es/docs/HumanGenomeBrowser/index.html?r=12:121113963-121213963 doesn't work anymore
Github: https://github.com/BioinfoUSAL/D3GB
Platform: Web
DNASkittle
Publication: (doi link) (2009) (# citations 6)
Tags: Exotic
Github: https://github.com/josiahseaman/skittle
Github Stargazers: 7
Platform: Web
EaSeq
https://easeq.net/screenshots/
Publication: (direct link) (doi link) (2016) (# citations 212)
Tags: Epigenomics
Platform: Desktop
FluentDNA
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7203487/
Publication: (doi link) (2020) (# citations 3)
Tags: Exotic
Platform: Web
Gambit
http://labsergen.langebio.cinvestav.mx/bioinformatics/jacob/?p=473
Tags: Alignments viewer, Linear
Platform: Desktop
Ribbon
Interactive: true
Publication: (direct link) (doi link) (2020) (# citations 44)
Language: JS
Tags: SV, Alignments viewer
Github: https://github.com/MariaNattestad/ribbon
Github Stargazers: 249
Platform: Web
GenomeSpy
Interactive: true
Github: https://github.com/genome-spy/genome-spy
Github Stargazers: 154
Platform: Web
Gnomad browser
https://github.com/macarthur-lab/gnomadjs
Publication: (doi link) (2020) (# citations 5772)
Language: JS
Tags: Linear, Population
Twitter: https://twitter.com/gnomad_project
Github Stargazers: 76
Platform: Web, Silo
Gremlin
http://compbio.cs.brown.edu/projects/gremlin/
Publication: (doi link) (2010) (# citations 22)
Platform: Web
GTEX Locus browser
https://gtexportal.org/home/locusBrowserPage/ACTN3
Publication: (doi link) (2020) (# citations 2270)
Tags: Expression, Linear, LD
Platform: Web
GWAS catalog browser
https://www.ebi.ac.uk/gwas/variants/rs1558902
Publication: (doi link) (2018) (# citations 3039)
Tags: Population, LD, GWAS
Twitter: https://twitter.com/gwascatalog?lang=en
Platform: Web
Hawkeye
Publication: (direct link) (doi link) (2007) (# citations 55)
Language: C++
Tags: Alignments viewer, Assembly QC
Github: https://github.com/peterhj/amos
Platform: Desktop
Human genome dating
https://human.genome.dating/region/chr1_13250000
Publication: (doi link) (2020) (# citations 117)
Language: JS
Tags: Population, GWAS
Note: made with vega/d3
Platform: Web
Icarus QUAST
http://quast.sourceforge.net/icarus.html
Publication: (doi link) (2016) (# citations 101)
Tags: Assembly QC, Graph
Github: https://github.com/ablab/quast
Github Stargazers: 357
Platform: Web
InGAP-SV
Publication: (doi link) (2011) (# citations 64)
Language: Java
Tags: SV, Alignments viewer
Platform: Desktop
Introgression browser
https://git.wageningenur.nl/aflit001/ibrowser
Publication: (direct link) (doi link) (2015) (# citations 17)
Language: Python
Tags: SV, Introgression
Platform: Web
IslandViewer and IslandPlot
https://bl.ocks.org/lairdm/c6c235dbfa6e6ee61565
Publication: (doi link) (2015) (# citations 250)
Tags: Microbiology, Circular, Linear
Note: web app using it here https://pathogenomics.sfu.ca/islandviewer uses D3, SVG
Github: https://github.com/lairdm/islandplot
Github Stargazers: 33
Platform: Web
MagicViewer
http://bioinformatics.zj.cn/magicviewer/
Publication: (direct link) (doi link) (2010) (# citations 40)
Language: Java
Tags: Alignment viewer
Platform: Desktop
Locuszoom
Publication: (doi link) (2010) (# citations 2152)
Tags: GWAS, Population
Github: https://github.com/statgen/locuszoom
Github Stargazers: 146
Platform: Web
Locuszoom.js
http://locuszoom.org/locuszoomjs.php
Publication: (doi link) (2021) (# citations 140)
Github: https://github.com/statgen/locuszoom
Github Stargazers: 146
Platform: Web
LookSeq
https://www.sanger.ac.uk/tool/lookseq/
Publication: (doi link) (2009) (# citations 50)
Tags: Alignments viewer
Github: https://github.com/magnusmanske/lookseq
Github Stargazers: 4
Platform: Web
Panoptes
https://www.malariagen.net/apps/ag1000g/phase1-AR3/index.html
Publication: (doi link) (2017) (# citations 6)
Tags: Population
Github: https://github.com/cggh/panoptes
Github Stargazers: 37
MapView
https://sites.google.com/site/wjwdavy/
Publication: (direct link) (doi link) (2009) (# citations 65)
Tags: Alignments viewer
Note: links in original paper are dead, but URL provided here works
Platform: Desktop
SeqCover
https://brentp.github.io/seqcover/#gene=AIFM1
Tags: Coverage
Github: https://github.com/brentp/seqcover
Github Stargazers: 49
Platform: Web
SEQing
https://github.com/malewins/SEQing
Publication: (doi link) (2020) (# citations 8)
Language: Python
Tags: Special-purpose
Github Stargazers: 8
Platform: Web
SFARI
https://gene.sfari.org/database/human-gene/
Publication: (doi link) (2010) (# citations 222)
Tags: CNV
Platform: Web, Silo
Short read assembly browser
Publication: (doi link) (2013) (# citations 557)
Tags: Alignments viewer
Platform: Web, Silo
SNPitty
https://bitbucket.org/ccbc/snpitty/src/master/
Publication: (direct link) (doi link) (2018) (# citations 13)
Language: R
Tags: CNV
Platform: Web
SNIPViz
Publication: (doi link) (2014) (# citations 7)
Github: https://github.com/yeastrc/snipviz
Github Stargazers: 19
Platform: Web
SplitThreader
Publication: (doi link) (2016) (# citations 10)
Github: https://github.com/MariaNattestad/SplitThreader
Github Stargazers: 66
Platform: Web
Staden
https://sourceforge.net/projects/staden/
Publication: (doi link) (2010) (# citations 186)
Tags: Alignments viewer, Assembly
Platform: Desktop
TASUKE
https://ricegenome.dna.affrc.go.jp/
Publication: (doi link) (2019) (# citations 20)
Tags: Pangenome
Note: info about multi-genome-browser https://tasuke.dna.affrc.go.jp/
Platform: Web
TE-nest
Publication: (doi link) (2007) (# citations 55)
Language: Perl
Tags: Transposons, Repeats, Deadlink
Note: this was an online tool that does not appear to exist anymore see https://web.archive.org/web/20170712104431/http://www.plantgdb.org/tool/TEnest/. the github link is re-hosted source code also downloaded from archive.org
Github: https://github.com/cmdcolin/TEnest
Github Stargazers: 1
Platform: Web, CGI, Server
Transposcope
Publication: (doi link) (2020) (# citations 0)
Language: JS
Tags: Transposons, Repeasts
Github: https://github.com/FenyoLab/transposcope
Github Stargazers: 6
Platform: Web
UGENE
Publication: (doi link) (2012) (# citations 1963)
Language: C++
Tags: Special-purpose
Github: https://github.com/ugeneunipro/ugene
Github Stargazers: 193
Platform: Desktop
Varsome
https://varsome.com/security-validation/?next=/variant/hg19/NM_000088.3(COL1A1):c.658C%3ET
Publication: (doi link) (2018) (# citations 1079)
Tags: Annotation
Platform: Web, Silo
Vials
Publication: (doi link) (2016) (# citations 15)
Tags: Splicing
Github: https://github.com/Caleydo/vials
Github Stargazers: 14
Platform: Web
wasm bigwig demo browser
https://shk656461.github.io/index.html
Language: WASM
Tags: Quantitative
Platform: Web
BasePlayer
Publication: (direct link) (doi link) (2018) (# citations 26)
Language: Java
Tags: General
Github: https://github.com/rkataine/BasePlayer
Github Stargazers: 4
Platform: Desktop
IGB
Publication: (direct link) (doi link) (2016) (# citations 300)
Language: Java
Tags: General, Alignments viewer
Platform: Desktop
IGV
Publication: (doi link) (2011) (# citations 10751)
Language: Java
Tags: General, Alignments viewer, SV, Quantitative
Github: https://github.com/igvteam/igv
Github Stargazers: 601
Platform: Desktop
Savant
http://bioinformatics-ca.github.io/savant_genome_browser_lab_2015/
Publication: (direct link) (doi link) (2012) (# citations 44)
Language: Java
Tags: General, SV, Alignments viewer
Github: https://github.com/compbio-UofT/savant
Github Stargazers: 12
Platform: Desktop
Tablet
https://ics.hutton.ac.uk/tablet/
Publication: (doi link) (2012) (# citations 744)
Language: Java
Tags: General, Alignments viewer
Github: https://github.com/cropgeeks/tablet
Github Stargazers: 36
Platform: Desktop
BigTop
https://blog.dnanexus.com/2019-05-21-bigtop-data-visualization/
Language: JS
Github: https://github.com/dnanexus/bigtop
Github Stargazers: 5
Platform: Web
Biodalliance
Publication: (doi link) (2011) (# citations 89)
Language: JS
Tags: General, Alignments viewer
Github: https://github.com/dasmoth/dalliance
Github Stargazers: 226
Platform: Web
Ensembl genome browser
https://useast.ensembl.org/Homo_sapiens/Location/View?r=17:63992802-64038237
Publication: (doi link) (2002) (# citations 1136)
Tags: General, Comparative
Platform: Web, Silo
GBrowse 2
Publication: (doi link) (2013) (# citations 100)
Language: Perl
Tags: General
Note: Original gbrowse paper https://doi.org/10.1101/gr.403602
Github: https://github.com/GMOD/GBrowse
Github Stargazers: 49
Platform: Web
GenomeMaps
Publication: (direct link) (doi link) (2013) (# citations 25)
Language: JS
Github: https://github.com/opencb/genome-maps
Github Stargazers: 39
Gosling
Publication: (doi link) (2022) (# citations 20)
Language: JS, WebGL, Typescript, React
Tags: General, Epigenomics, Higlass integration, Linear, Circular, Comparative, Quantitative
Github: https://github.com/gosling-lang/gosling.js
Github Stargazers: 154
Platform: Web
HiGlass
Publication: (doi link) (2018) (# citations 872)
Tags: General, Epigenomics, Hi-C
Github: https://github.com/higlass/higlass
Github Stargazers: 296
Platform: Web, Server
IGV.js
https://github.com/igvteam/igv.js/
Publication: (doi link) (2020) (# citations 43)
Language: JS
Tags: General, Alignments viewer
Github Stargazers: 614
Platform: Web
JBrowse
http://jbrowse.org/jbrowse1.html
Publication: (doi link) (2016) (# citations 606)
Language: JS
Tags: General, Alignments viewer, SV, Quantitative, Gene structure
Note: See also JBrowse plugin registry https://gmod.github.io/jbrowse-registry. Runs on the web or as a desktop app using Electron
Github: https://github.com/GMOD/jbrowse
Github Stargazers: 457
Platform: Web, Desktop
JBrowse 2
Publication: (doi link) (2022) (# citations 14)
Language: JS, Typescript, React
Tags: General, SV, Comparative, Dotplot, Circular, Alignments viewer, Quantitative, Hi-C
Note: See gallery for more examples https://jbrowse.org/jb2/gallery
Github: https://github.com/GMOD/jbrowse-components
Github Stargazers: 178
Platform: Web
Kero-BROWSE
https://kero.hgc.jp/examples/CLCL/hg38/index.html
Publication: (doi link) (2017) (# citations 43)
Language: JS
Tags: General, SV, Alignments viewer, Comparative
Note: Also can visualize basic synteny, see tracks e.g. https://kero.hgc.jp/tool/keyword.html#kero:chrX:153,724,868-153,744,762 human vs chimp
Github: https://github.com/DBKERO/genome_browser
Github Stargazers: 7
Platform: Web
NCBI Genome Data Viewer
https://www.ncbi.nlm.nih.gov/genome/gdv/
Publication: (doi link) (2020) (# citations 94)
Tags: General, SV, Epigenomics, Gene structure, Splicing
Platform: Web, Silo
Nucleome browser
https://vis.nucleome.org/v1/main.html
Publication: (doi link) (2022) (# citations 1)
Language: JS
Note: github at https://github.com/nucleome
Twitter: https://twitter.com/4DNucleome
Platform: Web
Pileup.js
https://github.com/hammerlab/pileup.js
Publication: (doi link) (2016) (# citations 18)
Language: JS
Github Stargazers: 271
Platform: Web
Trackster
https://galaxyproject.org/learn/visualization/
Publication: (doi link) (2012) (# citations 23)
Tags: General
Platform: Web
UCSC genome browser
Publication: (doi link) (2002) (# citations 5501)
Tags: General
Github: https://github.com/ucscGenomeBrowser/kent
Github Stargazers: 203
Platform: Web, Silo
Valis browser
Tags: General, Quantitative, Epigenomics, Deadlink
Github: https://github.com/VALIS-software/valis-hpgv
Github Stargazers: 13
Platform: Web
WashU epigenomics browser
https://epigenomegateway.wustl.edu/
Publication: (doi link) (2019) (# citations 213)
Tags: General, Epigenomics, Hi-C, Comparative
Note: The ReactJS is a redesign, there is also a legacy version. Note also, there are comparative features https://www.biorxiv.org/content/10.1101/2022.11.29.518374v1
Github: https://github.com/lidaof/eg-react
Github Stargazers: 65
Platform: Web
Zenbu
http://fantom.gsc.riken.jp/zenbu/
Publication: (doi link) (2014) (# citations 140)
Tags: General
Platform: Web
cgplot
https://github.com/dfguan/cgplot
Language: Python
Tags: Static, Dotplot, Comparative
Github Stargazers: 8
D-GENIES
http://dgenies.toulouse.inra.fr/
Publication: (doi link) (2018) (# citations 405)
Tags: Dotplot, Comparative
Github: https://github.com/genotoul-bioinfo/dgenies
Github Stargazers: 90
Platform: Web
Delly-maze
https://github.com/dellytools/maze
Publication: (doi link) (2012) (# citations 1656)
Language: Python
Tags: Dotplot, Static, Comparative
Note: see also https://www.gear-genomics.com/maze/
Github Stargazers: 9
Discoplot
https://github.com/mjsull/DiscoPlot
Publication: (doi link) (2015) (# citations 0)
Language: Python
Tags: Dotplot, Static, Comparative
Github Stargazers: 13
Dot
Tags: Dotplot, Comparative
Note: Python data preparation script
Github: https://github.com/MariaNattestad/dot
Github Stargazers: 30
Platform: Web
Dotlet
Publication: (doi link) (2000) (# citations 77)
Tags: Dotplot
Note: The original publication was 2000 but updated ~2020 with reactjs
Github: https://github.com/sib-swiss/dotlet
Github Stargazers: 4
Platform: Web
dotPlotly
https://github.com/tpoorten/dotPlotly/
Tags: Dotplot, Comparative
Github Stargazers: 180
Platform: Web
Dottup
https://www.bioinformatics.nl/cgi-bin/emboss/help/dottup
Tags: Dotplot
Note: also seen here http://eichlerlab.gs.washington.edu/pubs/chm1-structural-variation/data/GRCh37/heterochromatic_extensions.pdf
FlexiDot
https://github.com/molbio-dresden/flexidot
Publication: (doi link) (2018) (# citations 56)
Language: Python
Tags: Dotplot
Github Stargazers: 86
Platform: CLI
Gepard
http://cube.univie.ac.at/gepard
Publication: (doi link) (2007) (# citations 569)
Language: Java
Tags: Dotplot, Comparative
Github: https://github.com/univieCUBE/gepard
Github Stargazers: 57
Platform: Desktop
Jdot
https://github.com/LyonsLab/jdot
Language: JS
Tags: Dotplot, Comparative
Github Stargazers: 1
Platform: Web
mcutils
https://github.com/mchaisso/mcutils
Tags: Dotplot, Static, Comparative
Note: https://twitter.com/mjpchaisson/status/1040363992206569472
Github Stargazers: 12
Minidot
https://github.com/thackl/minidot
Language: R
Tags: Dotplot, Static, Comparative
Github Stargazers: 67
Mummer-idotplot
https://github.com/ryought/mummer-idotplot
Tags: Dotplot, Comparative
Github Stargazers: 25
Platform: Web, CLI
Mummerplot
http://mummer.sourceforge.net/
Publication: (doi link) (2004) (# citations 4256)
Language: GNUPlot
Tags: Dotplot, Static, Comparative
Github: https://github.com/mummer4/mummer
Github Stargazers: 406
Redotable
https://github.com/s-andrews/redotable
Language: Java
Tags: Dotplot, Comparative
Github Stargazers: 10
Platform: Desktop
syntenyPlotByR
https://github.com/shingocat/syntenyPlotByR
Language: R
Tags: Dotplot, Comparative, Static
Github Stargazers: 18
Chip Monk
http://www.bioinformatics.babraham.ac.uk/projects/chipmonk/
Publication: (doi link) (2007) (# citations 3)
Language: Java
Tags: Epigenomics
Note: Also see SeqMonk https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/
Platform: Desktop
Chipster
Publication: (doi link) (2011) (# citations 280)
Language: Java
Tags: Epigenomics, CNV
Note: Copy number tutorial https://chipster.csc.fi/manual/cn-tutorial.pdf
Github: https://github.com/chipster/chipster
Github Stargazers: 33
Platform: Desktop
cisGenome Browser
https://jhui2014.github.io/browser/screenshots.html
Publication: (doi link) (2010) (# citations 36)
Language: C
Tags: Epigenomics
Platform: Desktop
Epilogos
Language: Python
Tags: Epigenomics, Higlass integration
Github: https://github.com/meuleman/epilogos
Github Stargazers: 40
Platform: Web
Epiviz
Publication: (doi link) (2020) (# citations 4)
Tags: Epigenomics
Github: https://github.com/epiviz/epiviz
Github Stargazers: 66
Platform: Web
HiPiler
Publication: (doi link) (2018) (# citations 34)
Language: JS
Tags: Epigenomics, Hi-C, Higlass integration
Github: https://github.com/flekschas/hipiler
Github Stargazers: 13
Platform: Web
Juicebox
https://github.com/aidenlab/Juicebox
Publication: (direct link) (doi link) (2016) (# citations 1162)
Language: Java
Tags: Epigenomics, Hi-C
Github Stargazers: 223
Platform: Desktop
Juicebox.js
http://www.igv.org/doc/juiceboxjs.html
Publication: (direct link) (doi link) (2018) (# citations 257)
Language: JS
Tags: Epigenomics, Hi-C
Github: https://github.com/igvteam/juicebox.js
Github Stargazers: 19
Platform: Web
Peax
https://github.com/Novartis/peax
Publication: (doi link) (2020) (# citations 20)
Language: JS
Tags: Epigenomics, Higlass integration
Github Stargazers: 67
Platform: Web
eweitz/Ideogram
https://github.com/eweitz/ideogram
Language: JS
Tags: Ideogram
Github Stargazers: 271
Platform: Web
Ideogram
https://github.com/RCollins13/HumanIdiogramLibrary
Publication: (doi link)
Language: SVG
Github Stargazers: 84
karyoploteR
https://github.com/bernatgel/karyoploteR
Publication: (doi link) (2017) (# citations 484)
Language: R
Github Stargazers: 282
KaryotypeSVG
https://github.com/andreasprlic/karyotypeSVG
Tags: Ideogram
Github Stargazers: 6
Platform: Web
NCBI Genome Decoration
Tags: Ideogram
Note: Was located at https://www.ncbi.nlm.nih.gov/genome/tools/gdp/, sunsetted in 2023
Platform: Web, Form, Silo, Historical
UCSC Genome Graphs
http://genome.ucsc.edu/cgi-bin/hgGenome
Publication: (doi link) (2002) (# citations 5501)
Tags: Ideogram
Github: https://github.com/ucscGenomeBrowser/kent
Github Stargazers: 203
Platform: Web, Form, Silo
iGenomics
Publication: (doi link) (2020) (# citations 17)
Language: Objective-C
Tags: Mobile, Alignments viewer
Github: https://github.com/stuckinaboot/iGenomics
Github Stargazers: 36
Pan-Tetris
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547177/
Publication: (doi link) (2015) (# citations 15)
Tags: Pangenome
Panacaea
https://github.com/JCVenterInstitute/PanACEA
Publication: (doi link) (2018) (# citations 9)
Language: Perl
Tags: Pangenome
Github Stargazers: 6
Panache
https://github.com/SouthGreenPlatform/panache
Publication: (doi link) (2021) (# citations 9)
Tags: Pangenome
Github Stargazers: 41
panX
http://pangenome.tuebingen.mpg.de/
Publication: (direct link) (doi link) (2017) (# citations 186)
Tags: Pangenome
Github: https://github.com/neherlab/pan-genome-analysis
Github Stargazers: 125
RPAN (3kricedb)
http://cgm.sjtu.edu.cn/3kricedb/visualization/?tracks=DNA%2Cgene%2CPF
Publication: (doi link) (2016) (# citations 113)
Tags: Pangenome, JBrowse integration
Platform: Web
Protael
http://sanshu.github.io/protaelweb/
Publication: (direct link) (doi link) (2015) (# citations 8)
Language: JS
Github: https://github.com/sanshu/protaeljs
Github Stargazers: 18
Platform: Web
ProteinPaint
https://pecan.stjude.cloud/proteinpaint
Publication: (direct link) (doi link) (2015) (# citations 239)
Language: JS
Tags: Protein, Cancer, Lollipops, SV, Canvas
Github: https://github.com/stjude/proteinpaint
Github Stargazers: 12
Platform: Web
GenomePaint
https://genomepaint.stjude.cloud/
Publication: (direct link) (doi link) (2021) (# citations 18)
Tags: CNV, Linear, Cancer, Lollipops, SV, Alignments viewer
Note: Demos https://proteinpaint.stjude.org/bam/
Github: https://github.com/stjude/proteinpaint
Github Stargazers: 12
Platform: Web
pViz
https://github.com/Genentech/pviz
Publication: (doi link) (2014) (# citations 19)
Language: JS
Tags: Protein
Github Stargazers: 68
Platform: Web
UCSC Xena
Publication: (doi link) (2020) (# citations 1936)
Language: JS
Tags: Heatmap, Population
Github: https://github.com/ucscXena/ucsc-xena-client
Github Stargazers: 57
Platform: Web
VIVA
https://www.biorxiv.org/content/10.1101/589879v1.full.pdf
Publication: (doi link) (2019) (# citations 7)
Tags: Heatmap, Population, Variation
Github: https://github.com/compbiocore/VariantVisualization.jl
Github Stargazers: 79
Platform: Web
Dotter
https://sonnhammer.sbc.su.se/Dotter.html
Publication: (doi link) (1995) (# citations 475)
Tags: Dotplot
Platform: CLI
REPAVER
https://gitlab.com/gringer/bioinfscripts/
Publication: (direct link) (doi link)
Tags: Repeats, Dotplot, Static, Linear
Platform: CLI
LinearDisplay.pl
https://github.com/JCVenterInstitute/LinearDisplay
Publication: (doi link) (2019) (# citations 470)
Language: Perl
Tags: Comparative
Note: readme says to cite this paper
Github Stargazers: 4
Platform: CLI
Gview
https://server.gview.ca/examples
Publication: (doi link) (2010) (# citations 283)
Language: Perl, Java, Java web start
Tags: Circular, Linear, Pangenome, Microbiology
Platform: Web
FastANI
https://github.com/ParBLiSS/FastANI
Publication: (doi link) (2018) (# citations 2540)
Language: C++
Tags: Comparative, Microbiology
Github Stargazers: 342
covviz
https://brwnj.github.io/covviz/
Language: JS
Tags: CNV, Coverage, Population
Github: https://github.com/brwnj/covviz
Github Stargazers: 53
clinker
https://github.com/gamcil/clinker
Publication: (direct link) (doi link) (2021) (# citations 537)
Language: JS
Tags: Comparative, Gene order
Github Stargazers: 495
Platform: Web
PopSV
https://github.com/jmonlong/PopSV/blob/master/3-Visualization.md
Publication: (doi link) (2018) (# citations 41)
Language: R
Tags: Population, SV
Github: https://github.com/jmonlong/PopSV
Github Stargazers: 28
Platform: Web
Shasta
https://chanzuckerberg.github.io/shasta/ComputationalMethods.html#ReadGraph
Publication: (doi link) (2020) (# citations 328)
Language: C++
Tags: Graph
Note: Uses graphviz
Platform: Web, Localhost, CLI
LINX
https://github.com/hartwigmedical/hmftools/blob/master/linx/README.md
Publication: (doi link) (2019) (# citations 36)
Language: Java, Circos integration
Tags: Graph, SV, Breakends, Circular, Linear, Gene fusion, Cancer
Note: part of the PURPLE/GRIDSS/LINX pipeline
Github: https://github.com/hartwigmedical/hmftools
Github Stargazers: 169
PURPLE
https://github.com/hartwigmedical/hmftools/blob/master/purity-ploidy-estimator/README.md
Publication: (doi link) (2019) (# citations 36)
Note: intermutation-distance rainfall plots/katagesis plots are not technically in genomic coordinates, but do indicate genomic cluster of variatnts
Github: https://github.com/hartwigmedical/hmftools
Github Stargazers: 169
SMRT View
http://files.pacb.com/software/smrtanalysis/2.3.0/doc/smrtview/help/Webhelp/App_View_Epipro.htm
Tags: SV
Note: wiki page https://github.com/PacificBiosciences/DevNet/wiki/SMRT-View
Github: https://github.com/PacificBiosciences/DevNet
Github Stargazers: 113
sockeye
https://www.bcgsc.ca/resources/software/sockeye
Publication: (direct link) (doi link) (2004) (# citations 21)
Tags: Exotic, Comparative, Historical
spinteny
https://github.com/skinner/spinteny
Language: JS
Tags: Exotic, Comparative
Github Stargazers: 1
Internet Contig Explorer
https://www.bcgsc.ca/resources/software/ice
Publication: (direct link) (doi link) (2003) (# citations 19)
Tags: Historical
bcftools roh
https://samtools.github.io/bcftools/howtos/roh-calling.html
Publication: (doi link) (2016) (# citations 458)
Language: Python, C, Matplotlib
Tags: Static
Note: Plots runs of homozygosity, has interactive plot-roh.py helper too
Github: https://github.com/samtools/bcftools
Github Stargazers: 605
bcftools cnv
https://samtools.github.io/bcftools/howtos/cnv-calling.html
Language: Python, C, Matplotlib
Tags: CNV
Github: https://github.com/samtools/bcftools
Github Stargazers: 605
mocha
https://github.com/freeseek/mocha
Publication: (doi link) (2018) (# citations 265)
Tags: CNV
Note: Has a full analysis pipeline associated with end result visualizations
Github Stargazers: 73
ALVIS (MSA viewer)
https://www.ebi.ac.uk/research/goldman/software/alvis
Publication: (direct link) (doi link) (2016) (# citations 9)
Language: Java
Tags: MSA
Note: Introduces sequence bundles concept, also see web app version https://www.ebi.ac.uk/goldman-srv/sequencebundles/ source code https://bitbucket.org/schwarzlab/alvis/src/master/
ALVIS (chimeric alignment viewer)
https://github.com/SR-Martin/alvis
Publication: (direct link) (doi link) (2021) (# citations 12)
Language: Java
Github Stargazers: 18
genevisR
https://bioconductor.org/packages/release/bioc/vignettes/GenVisR/inst/doc/Intro.html
Publication: (doi link) (2016) (# citations 226)
Language: R
Tags: CNV
Github: https://github.com/griffithlab/GenVisR
Github Stargazers: 201
NanoMethViz
http://www.bioconductor.org/packages/release/bioc/html/NanoMethViz.html
Publication: (doi link) (2021) (# citations 8)
Language: R
Tags: Methylation
Github: https://github.com/Shians/NanoMethViz
Github Stargazers: 19
GfaViz
Publication: (direct link) (doi link) (2018) (# citations 18)
Language: C++
Tags: Graph
Github: https://github.com/ggonnella/gfaviz
Github Stargazers: 63
Nextclade
https://clades.nextstrain.org/
Publication: (doi link) (2021) (# citations 485)
Tags: Phylogenetics, Microbiology
Note: Related usage on nextstrain app also
vcfR
https://knausb.github.io/vcfR_documentation/
Publication: (doi link) (2016) (# citations 590)
Language: R
Tags: QC, Population, Coverage
Note: image shows chromoqc output
Github: https://github.com/knausb/vcfR
Github Stargazers: 231
asgart
Publication: (direct link) (doi link) (2018) (# citations 12)
Language: Rust
Tags: SV, Ideogram, Circular, Linear
Github: https://github.com/delehef/asgart
Github Stargazers: 28
MashMap
https://github.com/marbl/MashMap/blob/master/scripts/generateDotPlot
Publication: (doi link) (2018) (# citations 109)
Tags: Dotplot
Github: https://github.com/marbl/MashMap
Github Stargazers: 253
udon
https://github.com/ocxtal/udon
Language: Rust
Tags: Alignments viewer
Note: Uses an advanced data structure for pileup, so visually a basic example but likely just a small demo
Github Stargazers: 20
AnnoJ
https://brainome.ucsd.edu/howto_annoj.html
Language: JS
Tags: Methylation
Note: See list of instances of the browser here https://ecker.salk.edu/genome-browser/
Github: https://github.com/mukamel-lab/annoj_cndd
Platform: Web
methylartist
https://github.com/adamewing/methylartist
Publication: (doi link) (2021) (# citations 6)
Language: Python
Tags: Long reads, Methylation
Github Stargazers: 100
gingko
http://qb.cshl.edu/ginkgo/?q=/9EiUttUP0CBHs3WnuBa0
Publication: (doi link) (2015) (# citations 209)
Tags: Single cell, CNV
Github: https://github.com/robertaboukhalil/ginkgo
Github Stargazers: 46
Platform: Web
copynumber
https://www.bioconductor.org/packages/release/bioc/vignettes/copynumber/inst/doc/copynumber.pdf
Publication: (doi link) (2012) (# citations 231)
Language: R
Tags: CNV
copykat
https://github.com/navinlabcode/copykat/blob/master/vignettes/copycat-vignettes.pdf
Publication: (doi link) (2021) (# citations 295)
Language: R
Tags: Single cell, CNV
Github: https://github.com/navinlabcode/copykat
Github Stargazers: 179
scCNV_heatmap
https://github.com/StefanKurtenbach/scCNV_heatmap
Language: Python
Tags: Single cell, CNV
Github Stargazers: 3
casper
https://github.com/akdess/CaSpER
Publication: (direct link) (doi link) (2020) (# citations 90)
Language: R
Tags: Single cell, CNV
Github Stargazers: 75
RectChr
https://github.com/BGI-shenzhen/RectChr
Language: Binary blob, Perl
Tags: Comparative, Ideogram, Static, Limited code available
Github Stargazers: 70
LDBlockShow
https://github.com/BGI-shenzhen/LDBlockShow
Publication: (direct link) (doi link) (2020) (# citations 161)
Tags: GWAS, Population
Github Stargazers: 117
clinker (gene fusion software)
https://github.com/Oshlack/Clinker/
Publication: (direct link) (doi link) (2018) (# citations 16)
Language: R
Tags: Gene fusion
Github Stargazers: 49
arriba
https://github.com/suhrig/arriba
Publication: (direct link) (doi link) (2021) (# citations 206)
Tags: Gene fusion
Github Stargazers: 206
FusionInspector
https://github.com/FusionInspector/FusionInspector/wiki
Publication: (doi link) (2021) (# citations 3)
Tags: Gene fusion
Note: Uses igv.js
Github: https://github.com/FusionInspector/FusionInspector
Github Stargazers: 50
NeoLoopFinder
https://github.com/XiaoTaoWang/NeoLoopFinder
Publication: (doi link) (2021) (# citations 67)
Language: Python
Github Stargazers: 50
vega
http://vega.archive.ensembl.org/Homo_sapiens/Location/Chromosome?r=6-QBL
Publication: (doi link) (2004) (# citations 91)
Tags: Assembly, Historical, Genetic map
Note: Mentioned in https://www.biorxiv.org/content/10.1101/2021.07.02.450883v1.full.pdf also note: vega standards for vertebrate genome annotation database
Platform: Web
nightingale/protvista
https://ebi-webcomponents.github.io/nightingale/#/msa
Publication: (doi link) (2017) (# citations 56)
Language: JS, Typescript
Note: Used on InterProScan website https://www.ebi.ac.uk/interpro/
Github: https://github.com/ebi-webcomponents/nightingale
Github Stargazers: 113
Platform: Web
ArchR
https://www.archrproject.com/articles/Articles/tutorial.html
Publication: (doi link) (2021) (# citations 585)
Language: R
Tags: Single cell
Github: https://github.com/GreenleafLab/ArchR
Github Stargazers: 333
PGAP-X
Publication: (direct link) (doi link) (2018) (# citations 23)
Language: C++
Tags: Pangenome
Platform: Desktop
MAVIS
Publication: (doi link) (2018) (# citations 19)
Language: Python
Tags: Gene fusion, SV
Github: https://github.com/bcgsc/mavis
Github Stargazers: 67
ProViz
http://slim.icr.ac.uk/proviz/index.php
Publication: (direct link) (doi link) (2016) (# citations 67)
Language: JS
Note: See also alphafold visualization as tracks http://slim.icr.ac.uk/projects/alphafold?page=alphafold_proviz_homepage
SVPV
Publication: (direct link) (doi link) (2017) (# citations 8)
Language: Python
Github Stargazers: 29
wiggleplotr
http://bioconductor.org/packages/devel/bioc/vignettes/wiggleplotr/inst/doc/wiggleplotr.html
Language: R
Tags: Coverage
Github: https://github.com/kauralasoo/wiggleplotr
Github Stargazers: 32
pretzel
https://github.com/plantinformatics/pretzel
Publication: (doi link) (2019) (# citations 20)
Tags: Comparative, Genetic map
Github Stargazers: 38
splicejam
https://github.com/jmw86069/splicejam
Publication: (doi link) (2019) (# citations 61)
Language: R
Github Stargazers: 26
genomegraphs
http://bioconductor.org/packages/2.5/bioc/vignettes/GenomeGraphs/inst/doc/GenomeGraphs.pdf
Publication: (doi link) (2009) (# citations 52)
Language: R
Tags: Ideogram, Quantitative, Splicing
IdeoViz
https://www.bioconductor.org/packages/release/bioc/vignettes/IdeoViz/inst/doc/Vignette.pdf
Language: R
Tags: Ideogram, Quantitative, Splicing
Github: https://github.com/shraddhapai/IdeoViz
Github Stargazers: 1
Plotgardener
https://github.com/PhanstielLab/plotgardener/
Publication: (doi link) (2022) (# citations 38)
Language: R
Github Stargazers: 267
MIRA
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html
Publication: (doi link) (2004) (# citations 864)
Language: C++
Tags: Assembly, Alignments viewer, Historical
Note: orig paper also describes mira here http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.23.7465&rep=rep1&type=pdf
oxford-plots
https://github.com/jherrero/oxford-plots
Tags: Dotplot
Note: Has nice description of a synteny pipeline here https://github.com/jherrero/oxford-plots/blob/master/examples/pig_X_Y.txt
Github Stargazers: 11
IGGE
https://github.com/immersivegraphgenomeexplorer/IGGE
Publication: (doi link) (2021) (# citations 4)
Note: Not open source
Github Stargazers: 2
PipMaker
http://pipmaker.bx.psu.edu/pipmaker/
Publication: (doi link) (2000) (# citations 892)
Tags: Comparative, Repeats, Annotation
Note: See also MultiPipMaker http://pipmaker.bx.psu.edu/pipmaker/mpm-example/index.html
GraphAlignmentViewer
https://github.com/Illumina/GraphAlignmentViewer
Language: Python
Tags: Repeats
Github Stargazers: 31
MEGA-X
Publication: (doi link) (2021) (# citations 6040)
Language: Pascal
Tags: MSA, Phylogenetics
Note: original paper from 1994 but actively updated. requires EULA for download
Github: https://github.com/KumarMEGALab/MEGA-source-code
Github Stargazers: 3
Platform: Desktop
Haploview
https://www.broadinstitute.org/haploview/haploview
Publication: (doi link) (2004) (# citations 11543)
Language: Java
Tags: Population, LD
Platform: Desktop
AliTreeViz
https://www.npmjs.com/package/alitreeviz
Language: JS
Tags: MSA, Phylogenetics
Github: https://github.com/lipme/alitreeviz
Github Stargazers: 4
WGDI
https://github.com/SunPengChuan/wgdi
Publication: (direct link) (doi link) (2021) (# citations 42)
Language: Python
Tags: Comparative, Dotplot, Circular
Github Stargazers: 99
AmpliconArchitect
https://github.com/virajbdeshpande/AmpliconArchitect
Publication: (doi link) (2019) (# citations 154)
Language: Python
Note: The term amplicon refers essentially to extrachromosomal DNA in cancer
Github Stargazers: 122
PGV
https://github.com/ucrbioinfo/PGV
Publication: (direct link) (doi link) (2021) (# citations 4)
Language: Python
Tags: Pangenome, Dotplot, Comparative
Github Stargazers: 18
Platform: Web
REViewer
https://github.com/Illumina/REViewer
Publication: (direct link) (doi link) (2021) (# citations 3)
Language: C++
Tags: Repeats
Note: See also GraphAlignmentViewer, similar look and from illumina also
Github Stargazers: 67
Trackplot (R)
https://github.com/PoisonAlien/trackplot
Publication: (doi link) (2024) (# citations 0)
Language: R
Tags: Coverage, Gene structure, Epigenomics
Github Stargazers: 111
gcMapExplorer
https://github.com/rjdkmr/gcMapExplorer
Publication: (doi link) (2017) (# citations 24)
Language: Python
Tags: Hi-C
Github Stargazers: 21
BRIG
Publication: (direct link) (doi link) (2011) (# citations 2289)
Language: Java
Tags: Comparative, Circular
Github: https://github.com/happykhan/BRIG
Github Stargazers: 23
Platform: Desktop
Ideogram viewer
https://bioinformatics.mdanderson.org/public-software/ideogramviewer/
Language: JS
Tags: Ideogram
Platform: Web
GENESPACE
https://github.com/jtlovell/GENESPACE/
Publication: (doi link) (2022) (# citations 65)
Language: R
Tags: Comparative
Note: Includes a powerful analysis pipeline, worth reading the paper
Github Stargazers: 162
ggplot2 manhattan plot
https://danielroelfs.com/blog/how-i-create-manhattan-plots-using-ggplot/
Tags: GWAS
Note: This is not a preconfigured tool but a blog post tutorial with tidy data and ggplot2
ete
http://etetoolkit.org/gallery/
Publication: (doi link) (2016) (# citations 1509)
Language: Python
Tags: MSA, Phylogenetics
Github: https://github.com/etetoolkit/ete
Github Stargazers: 743
ggtree
https://github.com/YuLab-SMU/ggtree
Publication: (doi link) (2016) (# citations 2731)
Language: R
Tags: MSA, Phylogenetics, ggplot2
Note: see https://yulab-smu.top/treedata-book/chapter7.html?q=msa#msaplot for MSA example
Github Stargazers: 785
Phandango
https://jameshadfield.github.io/phandango/#/examples
Publication: (doi link) (2017) (# citations 389)
Language: JS
Tags: Pangenome, GWAS, MSA, Phylogenetics, Microbiology
Github: https://github.com/jameshadfield/phandango
Github Stargazers: 110
GeneViTo
http://athina.biol.uoa.gr/bioinformatics/GENEVITO/
Publication: (doi link) (2003) (# citations 7)
Language: Java
Tags: Microbiology, General
Platform: Desktop
RegulomeExplorer
http://explorer.cancerregulome.org/all_pairs/?dataset=TCGA_ACC
Language: JS
Github: https://github.com/cancerregulome/RegulomeExplorer
Github Stargazers: 4
Platform: Web
CGView
Publication: (doi link) (2008) (# citations 1030)
Language: JS
Tags: Circular, Microbiology
Note: See also CGView comparison tool and other related https://paulstothard.github.io/cgview_comparison_tool/
Github: https://github.com/paulstothard/cgview
Github Stargazers: 35
Platform: Web
miropeats
http://www.littlest.co.uk/software/bioinf/old_packages/miropeats/
Publication: (direct link) (doi link) (1995) (# citations 36)
Tags: Comparative, Repeats, Synteny, Historical
Note: image from 2021 paper https://www.biorxiv.org/content/10.1101/2021.12.08.471837v1.full.pdf
Slinker
https://github.com/Oshlack/Slinker
Publication: (direct link) (doi link) (2021) (# citations 2)
Language: Python
Note: See also, clinker (gene fusion software)
Github Stargazers: 17
syntenyPlotteR
https://github.com/marta-fb/syntenyPlotteR
Publication: (doi link) (2023) (# citations 1)
Tags: Comparative
Github Stargazers: 32
chromoMap
https://lakshay-anand.github.io/chromoMap/index.html
Publication: (direct link) (doi link) (2022) (# citations 74)
Language: R
Tags: Comparative, Ideogram
Github: https://github.com/Lakshay-Anand/chromoMap
Github Stargazers: 3
SafFire
https://mrvollger.github.io/SafFire/#ref=CHM13_v1.1&query=GRCh38
Language: JS
Tags: Comparative
Github: https://github.com/mrvollger/SafFire
Github Stargazers: 21
Gingr
https://harvest.readthedocs.io/en/latest/content/gingr.html
Publication: (doi link) (2014) (# citations 1177)
Language: C++
Tags: Phylogenetics, Comparative, Microbiology
Github: https://github.com/marbl/gingr
Github Stargazers: 13
StainedGlass
Publication: (doi link) (2022) (# citations 41)
Tags: Repeats, Heatmap, Higlass integration
Github: https://github.com/mrvollger/StainedGlass
Github Stargazers: 74
Platform: Web, CLI
SimpleSynteny
https://www.dveltri.com/simplesynteny/about.html
Publication: (doi link) (2016) (# citations 91)
Tags: Comparative
Platform: Web, Server
DAGchainer
http://dagchainer.sourceforge.net/
Publication: (doi link) (2004) (# citations 287)
Tags: Dotplot, Comparative
AutoGraph
http://autograph.genouest.org/
Publication: (doi link) (2006) (# citations 42)
Tags: Comparative, Deadlink, Historical
EvolutionHighway
http://eh-demo.ncsa.illinois.edu/
Tags: Comparative, Historical
Note: The 'evolutionary highway' image type is reproduced in some other packages e.g. https://github.com/marta-fb/syntenyPlotteR, paper https://doi.org/10.1126/science.1111387
Smash++
https://github.com/smortezah/smashpp
Publication: (doi link) (2020) (# citations 13)
Language: C++
Tags: Comparative
Github Stargazers: 55
plotsr
https://github.com/schneebergerlab/plotsr
Publication: (doi link) (2022) (# citations 4)
Language: Python
Tags: Comparative, SV
Note: Blurs the line between synteny and SV visualization, a good thing! see also https://github.com/schneebergerlab/syri
Github Stargazers: 250
drawProteins
Publication: (doi link) (2018) (# citations 40)
Tags: Protein
Github: https://github.com/brennanpincardiff/drawProteins
Github Stargazers: 32
IBS (Illustrator for Biological Sequences)
Publication: (doi link) (2015) (# citations 722)
Language: Java
Tags: Protein
Platform: Silo, Web, Desktop
PFAM generate_graphic
https://pfam.xfam.org/generate_graphic
Tags: Protein
Note: Also see guide here https://pfam.xfam.org/help#tabview=tab10
Platform: Silo, Web
SnoopCGH
http://snoopcgh.sourceforge.net/
Publication: (doi link) (2009) (# citations 8)
Language: Java
Genovar
http://genovar.sourceforge.net/
Publication: (doi link) (2012) (# citations 2)
Language: Java
Tags: CNV, ArrayCGH, Alignments viewer
GenomeMatcher
http://www.ige.tohoku.ac.jp/joho/gmProject/gmmanual.html
Publication: (doi link) (2008) (# citations 218)
Language: Objective-C
Tags: Comparative
Twitter: https://twitter.com/GenomeMatcher
Platform: Desktop, Mac
SynBrowse
Publication: (doi link) (2005) (# citations 53)
Language: Perl
Tags: Comparative, GBrowse integration
Platform: Web
Sybil
Publication: (doi link) (2007) (# citations 52)
Language: Perl
Tags: Comparative, GBrowse integration
Note: Download https://sourceforge.net/projects/sybil/
Platform: Web
SyntenyPortal
http://bioinfo.konkuk.ac.kr/synteny_portal/
Publication: (doi link) (2016) (# citations 38)
Language: JS
Tags: Comparative, Circular
Platform: Web
CHROMEISTER
Publication: (doi link) (2019) (# citations 23)
Tags: Comparative, Dotplot
Github: https://github.com/estebanpw/chromeister
Github Stargazers: 38
r2cat
Publication: (doi link) (2009) (# citations 104)
Language: Java
Tags: Comparative, Dotplot
Github: https://github.com/phuseman/r2cat
Github Stargazers: 3
Seaview
http://doua.prabi.fr/software/seaview
Publication: (doi link) (2009) (# citations 4543)
Language: C++
Tags: MSA, Phylogenetics
Platform: Desktop
SequenceServer
Publication: (doi link) (2019) (# citations 147)
Tags: BLAST, Comparative, Circular
Github: https://github.com/wurmlab/sequenceserver
Github Stargazers: 263
Platform: Web
numbat
https://kharchenkolab.github.io/numbat/
Publication: (doi link) (2022) (# citations 8)
Language: R
Tags: Single cell, CNV
Github: https://github.com/kharchenkolab/numbat
Github Stargazers: 139
ggtranscript
https://github.com/dzhang32/ggtranscript
Publication: (doi link) (2022) (# citations 1)
Language: R
Tags: Gene structure
Github Stargazers: 115
CIAlign
Publication: (doi link) (2022) (# citations 31)
Language: Python
Tags: MSA
Note: Has useful utility functions to clean gaps and trim MSAs
Github: https://github.com/KatyBrown/CIAlign
Github Stargazers: 101
CoolBox
Publication: (doi link) (2021) (# citations 18)
Language: Python
Tags: Epigenomics, Hi-C
Note: fork of pyGenomeTracks
Github: https://github.com/GangCaoLab/CoolBox
Github Stargazers: 211
Platform: CLI, Web
CNANorm
https://www.bioconductor.org/packages/release/bioc/html/CNAnorm.html
Publication: (doi link) (2011) (# citations 144)
Language: R
Tags: CNV
GECO
http://bioinfo.mikrobio.med.uni-giessen.de/geco2/GecoMainServlet
Publication: (doi link) (2006) (# citations 21)
Language: Java
Tags: Microbiology, Comparative
Platform: Web, Deadlink, No binary or source available
Orchestral
Publication: (doi link) (2013) (# citations 5)
SequenceSurveyor
https://graphics.cs.wisc.edu/Vis/SequenceSurveyor/index.html
Publication: (doi link) (2011) (# citations 35)
Language: Adobe AIR
Tags: Comparative
BactoGENIE
Publication: (doi link) (2015) (# citations 8)
Tags: Comparative, Microbiology, Large display, No binary or source available
PSAT
Publication: (doi link) (2008) (# citations 26)
Tags: Comparative, Deadlink, No binary or source available
Platform: Web, Silo
TreeBrowser (MicrobesOnline)
http://www.microbesonline.org/cgi-bin/treeBrowse.cgi?locus=17761
Publication: (doi link) (2009) (# citations 377)
Language: Perl
Tags: Comparative, GBrowse integration
Platform: Web, Silo
UTGB (University of Tokyo Genome Browser)
Publication: (doi link) (2009) (# citations 11)
Language: Java
Tags: General
Github: https://github.com/utgenome/utgb
Github Stargazers: 2
Platform: Web, Servlet
Combo
Publication: (doi link) (2006) (# citations 37)
Language: Java
Tags: Comparative
Note: Based on the tool 'Argo'
Consed
http://bozeman.mbt.washington.edu/consed/consed.html
Publication: (doi link) (1998) (# citations 2671)
CNSpector
https://github.com/PapenfussLab/CNspector
Publication: (doi link) (2019) (# citations 16)
Tags: CNV
Github Stargazers: 4
GenomicBreaks
https://oist.github.io/GenomicBreaks/articles/GenomicBreaks.html
Tags: Comparative, Dotplot
Github: https://github.com/oist/GenomicBreaks/
Github Stargazers: 3
GenomeSyn
https://github.com/jmsong2/GenomeSyn
Language: Perl
Tags: Comparative, Ideogram, Deadlink
Github Stargazers: 18
Platform: Web, Desktop
CMPlot
Publication: (doi link) (2021) (# citations 371)
Language: R
Tags: GWAS
Github: https://github.com/YinLiLin/CMplot
Github Stargazers: 467
chromPlot
https://www.bioconductor.org/packages/release/bioc/vignettes/chromPlot/inst/doc/chromPlot.pdf
Publication: (doi link) (2016) (# citations 43)
Language: R
PhenoGram
https://ritchielab.org/software/phenogram-downloads
Publication: (doi link) (2013) (# citations 167)
Language: Ruby
Tags: Ideogram
Note: Can be web server or download
Platform: Web, Silo, CLI
RIdeogram
https://github.com/TickingClock1992/RIdeogram
Publication: (doi link) (2020) (# citations 246)
Language: R
Tags: Ideogram, Comparative
Github Stargazers: 144
CrowsNest
https://pgsb.helmholtz-muenchen.de/crowsnest/help.html
Publication: (doi link) (2016) (# citations 1)
Tags: Comparative
ERGO
Publication: (direct link) (doi link) (2003) (# citations 165)
Tags: Commercial, MSA, SV, Coverage, Alignments viewer, Comparative, Annotation, Variation, Expression
modbamtools
https://github.com/rrazaghi/modbamtools
Publication: (doi link) (2022) (# citations 9)
Language: Python
Tags: Methylation, Epigenomics
Github Stargazers: 41
sequenza
https://cran.r-project.org/web/packages/sequenza/vignettes/sequenza.html#plots-and-results
Publication: (doi link) (2015) (# citations 562)
Language: R
Tags: CNV
Note: also see https://sequenzatools.bitbucket.io/#/home
pyCircos
https://github.com/ponnhide/pyCircos
Language: Python
Tags: Circular
Note: See also https://github.com/ponnhide/plasmidviewer
Github Stargazers: 294
GeneticsMakie.jl
https://github.com/mmkim1210/GeneticsMakie.jl
Publication: (doi link) (2022) (# citations 2)
Language: Julia
Tags: GWAS, Gene structure, LD
Github Stargazers: 69
fineSTRUCTURE aka ChromoPainter
http://www.paintmychromosomes.com/
Publication: (doi link) (2012) (# citations 915)
Tags: Local ancestry
MOSAIC
https://maths.ucd.ie/~mst/MOSAIC/
Publication: (doi link) (2019) (# citations 50)
Language: R
Tags: Local ancestry
Prosite/MyDomains
https://prosite.expasy.org/mydomains
Publication: (doi link) (2007) (# citations 342)
Tags: Protein
Platform: Web, Silo
snpit
https://github.com/aineniamh/snipit
Language: Python
Tags: Variation, Population
Github Stargazers: 104
local-rearrangements
https://github.com/mcfrith/local-rearrangements
Language: Python
Note: Can color dotplots with annotations for e.g. exons, transposons, low complexity regions. See also last-dotplot. Nice figure using it here https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-020-00762-1/figures/4
Github Stargazers: 11
GeCoViz
Publication: (doi link) (2022) (# citations 6)
Tags: Microbiology, Comparative
Platform: Web, Silo
multiGenomicContext
https://github.com/Sanrrone/multiGenomicContext
Tags: Comparative
Github Stargazers: 7
ggmsa
Publication: (doi link) (2022) (# citations 66)
Language: R
Tags: MSA
Note: See also ggtree
Github: https://github.com/YuLab-SMU/ggmsa
Github Stargazers: 190
AccuSyn
Language: JS
Tags: Comparative
Github: https://github.com/jorgenunezsiri/accusyn
Github Stargazers: 15
CView
https://sourceforge.net/projects/cview/
Publication: (doi link) (2022) (# citations 0)
Language: Java
Tags: MSA
signac
https://github.com/timoast/signac/
Publication: (doi link) (2021) (# citations 574)
Language: R
Tags: Coverage, Single cell
Github Stargazers: 283
pyGenomeViz
https://github.com/moshi4/pyGenomeViz
Language: Python
Tags: Comparative
Note: See also https://github.com/moshi4/MGCplotter https://github.com/moshi4/GBKviz https://github.com/moshi4/plot_genome_align_fig
Github Stargazers: 215
SODA
Publication: (doi link)
Language: JS, Typescript
Tags: Repeats, Circular, Linear
Note: Describes itself as a low-level library to create larger applications with
Github: https://github.com/sodaviz/soda
Github Stargazers: 5
JBR
https://artyomovlab.wustl.edu/jbr/2018_h3k27ac_aging/
Language: Java
Tags: Epigenomics
Note: Not open source, at least not on github
Github: https://github.com/Jetbrains-Research/jbr
Github Stargazers: 11
clonifier
Language: Rust, Typescript, React
Tags: Microbiology, Synthetic biology
Github: https://github.com/dlesl/clonifier
Github Stargazers: 5
ctag
Tags: Graph, Population
Note: See also hygene https://github.com/ProgrammingLife2017/hygene
Github: https://github.com/AbeelLab/ctag
Github Stargazers: 1
vcfPlotein
https://vcfplotein.liigh.unam.mx/#/
Tags: Variation
Github: https://github.com/redcpp/vcfplotein
Github Stargazers: 6
CoveragePlotter
http://lindenb.github.io/jvarkit/CoveragePlotter.html
Language: Java
Note: See also http://lindenb.github.io/jvarkit/WGSCoveragePlotter.html for multi-chromosome
tagore
https://github.com/jordanlab/tagore
Language: Python
Tags: Ideogram, Local ancestry, Chromosome painting
Github Stargazers: 33
ggcoverage
https://cran.r-project.org/web/packages/ggcoverage/vignettes/ggcoverage.html
Publication: (doi link) (2022) (# citations 1)
Language: R
Tags: Coverage, Ideogram, CNV, Splicing
Github: https://github.com/showteeth/ggcoverage
Github Stargazers: 194
ezcharts
Language: Python
Tags: Ideogram
Github: https://github.com/epi2me-labs/ezcharts
Github Stargazers: 12
pyCirclize
Language: Python
Tags: Circular
Github: https://github.com/moshi4/pyCirclize
Github Stargazers: 535
plasmapR
Language: R
Tags: Synthetic biology, Circular
Github: https://github.com/BradyAJohnston/plasmapR
Github Stargazers: 68
DrukBam
Language: Python
Tags: Alignments viewer
Github: https://github.com/StephanHolgerD/DrukBam
Github Stargazers: 16
genome_coverage_plotter
Language: Python
Github: https://github.com/matted/genome_coverage_plotter
Github Stargazers: 6
PGR-TK
Publication: (doi link) (2023) (# citations 7)
Language: Rust
Github: https://github.com/cschin/pgr-tk
Github Stargazers: 10
asynt
Language: R
Tags: Comparative, Dotplot
Github: https://github.com/simonhmartin/asynt
Github Stargazers: 22
GeMo
Publication: (doi link) (2022) (# citations 2)
Language: JS
Tags: Chromosome painting, Ideogram
Github: https://github.com/SouthGreenPlatform/GeMo
Github Stargazers: 12
NGenomeSyn
Publication: (doi link) (2023) (# citations 18)
Language: Perl
Tags: Comparative, Multi-way synteny, Synteny
Note: See also RectChr
Github: https://github.com/hewm2008/NGenomeSyn
Github Stargazers: 129
chromsyn
Language: R
Tags: Comparative, Synteny, Multi-way
Github: https://github.com/slimsuite/chromsyn
Github Stargazers: 21
pixy
https://pixy.readthedocs.io/en/latest/plotting.html#a-genome-wide-plot-of-summary-statistics
Tags: Population, Variation
Note: The link in readthedocs shows a nice general purpose way to plot multi-chromosome plots in ggplot2 with facet grid. Alternative methods for multi-chromosome plots shown by the manhattan ggplot2 tutorial (https://danielroelfs.com/blog/how-i-create-manhattan-plots-using-ggplot/ uses cumulative bp instead of facet_grid)
Github: https://github.com/ksamuk/pixy/
Github Stargazers: 94
vcf2circos
https://github.com/bioinfo-chru-strasbourg/vcf2circos
Note: Based on PCircos https://github.com/CJinny/PCircos
Github Stargazers: 24
OmicCircos
http://bioconductor.org/packages/release/bioc/html/OmicCircos.html
Publication: (doi link) (2014) (# citations 133)
Language: R
Tags: Circular, CNV, Comparative, SV, Coverage
Github: https://github.com/CBIIT-CGBB/OmicCircos2
Github Stargazers: 3
ABrowse (genome browser)
Publication: (doi link) (2012) (# citations 17)
Language: JavaScript
Tags: General, Historical
Note: Had integrations with BioMart, Taverna
Platform: Web
VRPG
https://github.com/codeatcg/VRPG
Publication: (doi link) (2023) (# citations 0)
Github Stargazers: 18
Platform: Web
Taxonium
Publication: (doi link) (2022) (# citations 27)
Language: JavaScript, Python
Tags: Phylogenetics, Microbiology
Note: Genome variation visualisation in Taxonium is provided by the 'Treenome Viewer': https://academic.oup.com/bioinformatics/article/39/1/btac772/6858450
Github Stargazers: 86
Platform: Web
MosaicCatcher pipeline
Language: R, Python, SnakeMake
Tags: Single cell, Strand-seq
Github: https://github.com/friendsofstrandseq/mosaicatcher-pipeline
Github Stargazers: 20
ReConPlot
Publication: (doi link) (2023) (# citations 1)
Language: R
Github: https://github.com/cortes-ciriano-lab/ReConPlot
Github Stargazers: 16
rich-msa
Language: Python
Tags: Text-based, MSA
Github: https://github.com/althonos/rich-msa
Github Stargazers: 74
gtracks
https://gitlab.com/salk-tm/gtracks
Language: Python
Tags: General
Note: Powered by pyGenomeTracks
bamscope
https://github.com/jslfree080/bamscope
Language: Kotlin
Tags: Alignments viewer
Github Stargazers: 7
syntR
https://www.samuklab.com/syntR/articles/syntr_tutorial.html
Language: R
Tags: Comparative, Dotplot
Github: https://github.com/ksamuk/syntR
Github Stargazers: 4
GCSnap
Publication: (doi link) (2021) (# citations 6)
Language: Python
Tags: Comparative, Synteny
Github: https://github.com/JoanaMPereira/GCsnap
Github Stargazers: 19
trackplot (python)
https://github.com/ygidtu/trackplot
Publication: (doi link) (2023) (# citations 0)
Language: Python
Tags: General, Gene structure, Sashimi
Github Stargazers: 58
ModDotPlot
https://github.com/marbl/ModDotPlot
Language: Python
Tags: Comparative, Heatmap, Repeats
Github Stargazers: 62
odp (oxford dot plots)
https://github.com/conchoecia/odp
Publication: (doi link) (2023) (# citations 73)
Language: Python
Tags: Comparative, Macrosynteny, Synteny, Snakemake
Note: Pub is not for visualization tool, but it is suggested to cite this paper
Github Stargazers: 98
genoVi
https://github.com/robotoD/GenoVi
Publication: (doi link) (2023) (# citations 12)
Language: Python
Tags: Circular, Comparative, Microbiology
Github Stargazers: 62
TRVZ (TRGT tandem repeat genotyping visualizer)
https://github.com/PacificBiosciences/trgt
Publication: (doi link) (2023) (# citations 7)
Language: Rust
Github Stargazers: 83
BRICK (BRIG-like circular knowledgebase)
Language: JS
Tags: Circular, Comparative, Microbiology
Note: See also BRIG
Github: https://github.com/esteinig/brick
Github Stargazers: 9
SGTK (scaffold graph toolkit)
https://olga24912.github.io/SGTK/
Interactive: true
Publication: (doi link) (2018) (# citations 8)
Tags: Graph
Github: https://github.com/olga24912/SGTK
Github Stargazers: 26
VAG
Publication: (doi link) (2023) (# citations 0)
Github: https://github.com/lipingfangs/VAG
Github Stargazers: 16
ntSynt
https://github.com/bcgsc/ntSynt/tree/main/visualization_scripts
Publication: (doi link) (2024) (# citations 0)
Language: R
Tags: Comparative, Synteny, Multi-way synteny
Note: Uses gggenomes
Github: https://github.com/bcgsc/ntSynt/
Github Stargazers: 37
geneviewer
https://nvelden.github.io/geneviewer/
Language: R
Tags: Static, Comparative
Github: https://github.com/nvelden/geneviewer
Github Stargazers: 4
Note: if you would like your tool removed or screenshot removed (for copyright purposes for example) let me know