awesome-genome-visualization

https://github.com/calipho-sib/feature-viewer

FeatureViewer

Publication: (doi link)

https://jrderuiter.github.io/geneviz/usage.html

Github Stargazers: 98

Platform: Web

Geneviz

Language: Python

http://software.broadinstitute.org/software/genomestrip/

Github: https://github.com/jrderuiter/geneviz

Github Stargazers: 14

Genome STRiP

Publication: (doi link) (2015) (# citations 288)

Tags: Static

GenomeTools

http://genometools.org/

Publication: (doi link) (2013) (# citations 245)

Language: C

https://github.com/nspies/genomeview

Github: https://github.com/genometools/genometools

Github Stargazers: 230

GenomeView

Publication: (doi link) (2018) (# citations 2)

Language: Python

Tags: Static, SV, Alignment viewer

Github Stargazers: 120

GenomeView (java app)

https://genomeview.org/content/quick-start-guide

Publication: (doi link) (2011) (# citations 106)

Language: Java

http://genoplotr.r-forge.r-project.org/

Github: https://github.com/GenomeView/genomeview

Github Stargazers: 5

genoPlotR

Publication: (doi link) (2010) (# citations 446)

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 211)

Language: R, ggplot2

Tags: Static, Ideogram, Circular, Multi

Github: https://github.com/lawremi/ggbio

Github Stargazers: 91

GGgenes

https://github.com/wilkox/gggenes

Language: R, ggplot2

Tags: Static, Comparative

Github Stargazers: 304

GGsashimi

https://github.com/guigolab/ggsashimi

Publication: (doi link) (2018) (# citations 89)

Language: R, ggplot2

Tags: Static

Github Stargazers: 83

GSSPlayground

https://github.com/orangeSi/GSSplayground

Language: Perl

Tags: Comparative, Static, Alignment viewer

Github Stargazers: 24

gtrellis

http://bioconductor.org/packages/devel/bioc/vignettes/gtrellis/inst/doc/gtrellis.html

Publication: (doi link) (2016) (# citations 12)

Language: R

Tags: Static, Ideogram, Quantitative, CNV

Github: https://github.com/jokergoo/gtrellis

Github Stargazers: 35

Gviz

https://bioconductor.org/packages/release/bioc/html/Gviz.html

Publication: (doi link) (2016) (# citations 473)

Language: R

Tags: Static, Alignment viewer, Quantitative, Multi

Github: https://github.com/ivanek/Gviz

Github Stargazers: 39

Hagfish

https://github.com/mfiers/hagfish/wiki/Plots

Language: Python

Tags: Static, Coverage

Github: https://github.com/mfiers/hagfish

Github Stargazers: 34

HiCPlotter

https://github.com/kcakdemir/HiCPlotter

Publication: (doi link) (2015) (# citations 123)

Language: Python

Tags: Static, Hi-C

Github Stargazers: 6

JVarKit/BamToSVG

http://lindenb.github.io/jvarkit/BamToSVG.html

Publication: (doi link)

Language: Java

Tags: Static, Alignment viewer

Lollipops

https://github.com/joiningdata/lollipops

Language: Go

Tags: Static, Protein, Lollipops

Github Stargazers: 160

Mason

http://www.yeastrc.org/mason/

Tags: Static, Protein

Platform: Web, Deadlink

Methplotlib

https://github.com/wdecoster/methplotlib

Publication: (doi link) (2020) (# citations 19)

Language: Python

Tags: Static, Epigenomics, Methylation

Github Stargazers: 67

Millefy

https://github.com/yuifu/millefy

Publication: (doi link) (2020) (# citations 3)

Language: R

Tags: Single cell

Github Stargazers: 21

Platform: Package

Pairoscope

http://pairoscope.sourceforge.net/

Language: C++

Tags: Static, SV

pauvre

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6991124/figure/fig-3/

Publication: (doi link) (2020) (# citations 7)

Language: Python

Tags: Static, Misc QC, Comparative

Github: https://github.com/conchoecia/pauvre

Github Stargazers: 41

Platform: CLI

PureScript genetics browser

https://github.com/chfi/purescript-genetics-browser

Language: Purescript

Tags: GWAS

Github Stargazers: 5

Platform: Web

screenshot of PureScript genetics browser

pyGenomeTracks

https://github.com/deeptools/pyGenomeTracks

Publication: (doi link) (2020) (# citations 77)

Language: Python

Tags: Static, Hi-C

Github Stargazers: 578

RACER

https://oliviasabik.github.io/RACERweb/articles/IntroToRACER.html

Publication: (doi link) (2018) (# citations 3)

Language: R

Tags: Static, GWAS

Github: https://github.com/oliviasabik/RACER

Github Stargazers: 11

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: 1

Samplot

https://github.com/ryanlayer/samplot

Publication: (doi link) (2021) (# citations 12)

Language: Python

Tags: Static, SV, Alignment viewer

Github Stargazers: 366

SashimiPlot

https://miso.readthedocs.io/en/fastmiso/sashimi.html

Publication: (doi link) (2015) (# citations 105)

Language: Python

Tags: Static, Expression, Splicing

Github: https://github.com/yarden/MISO

Github Stargazers: 124

shabam

https://github.com/dlrice/shabam

Language: Python

Tags: Static

Github Stargazers: 6

shinyChromosome

http://150.109.59.144:3838/shinyChromosome/

Publication: (direct link) (doi link) (2019) (# citations 10)

Language: R, Shiny

Tags: Dotplot, Linear, Ideogram

Github: https://github.com/YaoLab-Bioinfo/shinyChromosome

Github Stargazers: 35

Platform: Web

SparK

https://github.com/harbourlab/SparK

Publication: (direct link) (doi link) (2019) (# citations 14)

Language: Python

Tags: Static, Hi-C, Quantitative

Github Stargazers: 82

Spliceclust

https://github.com/pkimes/spliceclust

Language: R

Tags: Static, Splicing

Github Stargazers: 11

Sushi

https://www.bioconductor.org/packages/release/bioc/vignettes/Sushi/inst/doc/Sushi.pdf

Publication: (doi link) (2014) (# citations 142)

Language: R

Tags: Static, Multi

Github: https://github.com/PhanstielLab/Sushi

Github Stargazers: 58

svist4get

https://link.springer.com/article/10.1186/s12859-019-2706-8

Publication: (doi link) (2019) (# citations 24)

Language: Python

Tags: Static

svv

https://github.com/ryanlayer/svv

Language: Python

Tags: Static, SV, Coverage

Github Stargazers: 25

svviz

https://github.com/svviz/svviz

Publication: (doi link) (2015) (# citations 14)

Language: Python

Tags: Static, SV, Insertion

Github Stargazers: 74

svviz2

https://github.com/nspies/svviz2

Publication: (doi link) (2015) (# citations 14)

Language: Python

Tags: Static, SV, Insertion

Github Stargazers: 35

TnT

https://tnt.marlin.pub/articles/introduction

Publication: (doi link) (2016) (# citations 3)

Language: R, JS

Tags: Gene structure

Github: https://github.com/tntvis/tnt.genome

Github Stargazers: 16

Platform: Web, Interactive

trackViewer

https://bioconductor.org/packages/release/bioc/vignettes/trackViewer/inst/doc/trackViewer.html

Publication: (doi link) (2019) (# citations 64)

Language: R

Tags: Static, Lollipops, Quantitative

Github: https://github.com/jianhong/trackViewer

Github Stargazers: 34

Aequatus

https://github.com/TGAC/Aequatus

Publication: (doi link) (2018) (# citations 1)

Language: JS, Java

Tags: Comparative, Deadlink?

Github Stargazers: 7

Platform: Web, Silo

AliTV

https://alitvteam.github.io/AliTV/d3/AliTV.html

Publication: (doi link) (2017) (# citations 39)

Language: JS, D3, Perl

Tags: Comparative

Platform: Web

Artemis comparison tool (ACT)

https://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act

Publication: (doi link) (2005) (# citations 1259)

Language: Java

Tags: Comparative

Github: https://github.com/sanger-pathogens/Artemis

Github Stargazers: 171

Platform: Desktop

screenshot of Artemis comparison tool (ACT)

Biodalliance comparative demo

http://biodalliance.org/dev/test-comparative.html

Publication: (doi link) (2011) (# citations 87)

Language: JS

Tags: Comparative

Github: https://github.com/dasmoth/dalliance

Github Stargazers: 217

Platform: Web

screenshot of Biodalliance comparative demo

Chromatiblock

https://github.com/mjsull/chromatiblock

Publication: (direct link) (doi link) (2020) (# citations 1)

Language: Python

Tags: Comparative, Pangenome, Microbiology

Github Stargazers: 21

Platform: Web

CMap

http://gmod.org/wiki/CMap

Publication: (doi link) (2009) (# citations 63)

Language: Perl

Tags: Comparative

Github: https://github.com/gmod/cmap

Github Stargazers: 4

Platform: Web

CoGe

https://genomevolution.org/coge/

Publication: (doi link) (2017) (# citations 77)

Language: Perl

Tags: Comparative, Dotplot, Linear, JBrowse integration

Github: https://github.com/LyonsLab/coge

Github Stargazers: 41

Platform: Web, Silo

Comparative assembly hub / "snake track"

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296145/

Publication: (direct link) (doi link) (2014) (# citations 24)

Tags: Comparative, UCSC integration

Platform: Web

screenshot of Comparative assembly hub / "snake track"

CrossBrowse

https://github.com/shenkers/CrossBrowse

Publication: (direct link) (doi link) (2018) (# citations 0)

Language: Java

Tags: Comparative

Github Stargazers: 9

Platform: Desktop

CVit

https://sourceforge.net/projects/cvit/

Publication: (doi link) (2011) (# citations 23)

Language: Perl

https://github.com/LegumeFederation/cvitjs

Github: https://github.com/ekcannon/CViT

Github Stargazers: 1

Platform: Web

Cvit.js

Language: JS

https://mjsull.github.io/Easyfig/

Github Stargazers: 10

Platform: Web

EasyFig

Publication: (direct link) (doi link) (2011) (# citations 1779)

Language: Python

Tags: Comparative

Github: https://github.com/mjsull/Easyfig

Github Stargazers: 63

Platform: CLI

Edinburgh-Genome-Foundry/DnaFeaturesViewer

https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer

Publication: (direct link) (doi link) (2020) (# citations 32)

Language: Python

Tags: Microbiology, Synthetic biology

Github Stargazers: 399

Platform: Desktop

screenshot of Edinburgh-Genome-Foundry/DnaFeaturesViewer

GBrowse_syn

http://gmod.org/wiki/GBrowse_syn

Publication: (doi link) (2010) (# citations 29)

Language: Perl

Tags: Comparative

Github: https://github.com/GMOD/GBrowse

Github Stargazers: 46

Platform: Web

Genome Context Viewer

https://www.legumefederation.org/gcv/phytozome_10_2/

Publication: (doi link) (2017) (# citations 17)

Language: JS, Typescript

Tags: Comparative, Gene order

Github: https://github.com/legumeinfo/gcv

Github Stargazers: 20

Platform: Web, Silo

Genome-plots-processing

https://github.com/filip-husnik/genome-plots-processing

Publication: (doi link) (2016) (# citations 174)

Language: Processing

Tags: Comparative

Genomicus

https://www.genomicus.biologie.ens.fr/genomicus/

Publication: (doi link) (2021) (# citations 5)

Tags: Comparative, Ideogram, Dotplot

Platform: Web, Silo

gggenomes

https://github.com/thackl/gggenomes

Publication: (doi link) (2020) (# citations 1)

Language: R

Tags: Comparative

Github Stargazers: 335

Platform: Package

GIVE

https://zhong-lab-ucsd.github.io/GIVE_homepage/

Publication: (doi link) (2018) (# citations 14)

Language: JS

Tags: Comparative, Linear, Quantitative

Github: https://github.com/Zhong-Lab-UCSD/Genomic-Interactive-Visualization-Engine

Github Stargazers: 129

Platform: Web

mauve-viewer

https://github.com/nconrad/mauve-viewer

Language: JS

Tags: Comparative

Github Stargazers: 28

Platform: Web

MCScan (python version)

https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)

Publication: (doi link) (2015) (# citations 252)

Language: Python

Tags: Comparative, Dotplot, Linear

Github: https://github.com/tanghaibao/jcvi

Github Stargazers: 518

Platform: CLI

MCScanX

https://github.com/wyp1125/MCScanX

Publication: (doi link) (2012) (# citations 2151)

Language: Perl

Tags: Comparative, Dotplot, Circular, Linear, Ideogram

Github Stargazers: 128

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

screenshot of mGSV (multiple genome synteny viewer)

MizBee

http://www.cs.utah.edu/~miriah/mizbee/Overview.html

Publication: (direct link) (doi link) (2009) (# citations 102)

Language: Processing

Tags: Comparative

Platform: Desktop

Multiple genome viewer

http://www.informatics.jax.org/mgv/

Publication: (doi link) (2021) (# citations 1)

Language: JS, VueJS

Tags: Comparative

Github: https://github.com/mgijax/mgv

Github Stargazers: 7

Platform: Web, Silo

OMA local synteny browser

https://omabrowser.org/oma/synteny/ADH1A_HUMAN/

Publication: (doi link) (2020) (# citations 42)

Tags: Comparative, Gene order

Platform: Web, Silo

pafr

https://github.com/dwinter/pafr

Language: R, ggplot2

Tags: Comparative, Dotplot, Linear

Github Stargazers: 46

Parasight

https://baileylab.brown.edu/parasight/galframe.html

Publication: (doi link) (2005) (# citations 713)

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: 11

Platform: Desktop

SyMap

http://www.agcol.arizona.edu/software/symap/

Publication: (doi link) (2006) (# citations 134)

Tags: Comparative, Dotplot, Linear

Platform: Desktop

Synima

https://github.com/rhysf/Synima

Publication: (doi link) (2017) (# citations 30)

Language: Perl

Tags: Comparative

Github Stargazers: 49

Platform: CLI

Synteny browser

https://github.com/TheJacksonLaboratory/syntenybrowser

Tags: Comparative

Github Stargazers: 3

Platform: Web

SynTView

http://hub18.hosting.pasteur.fr/SynTView/documentation/

Publication: (direct link) (doi link) (2013) (# citations 20)

Tags: Comparative, Dotplot, Linear, Microbiology

Platform: Desktop, Web, Flash

SynVisio

https://synvisio.github.io/

Language: JS, D3

Tags: Comparative, Linear, Dotplot

Github: https://github.com/kiranbandi/synvisio

Github Stargazers: 54

Tripal MapViewer

Publication: (doi link) (2019) (# citations 3)

http://pipeline.lbl.gov/cgi-bin/gateway2

Github: https://github.com/statonlab/tripal_map

Github Stargazers: 1

VISTA browser

Publication: (doi link) (2004) (# citations 1354)

Tags: Comparative

Platform: Web, Silo

XMatchView

https://www.bcgsc.ca/resources/software/xmatchview

Publication: (doi link) (2018) (# citations 2)

Language: Python

Tags: Comparative

Github: https://github.com/bcgsc/xmatchview

Github Stargazers: 34

Platform: Desktop

AGB assembly graph browser

https://almiheenko.github.io/AGB/index.html

Publication: (direct link) (doi link) (2019) (# citations 10)

Language: Python

Tags: Graph

Github: https://github.com/almiheenko/AGB

Github Stargazers: 61

Platform: Web

No screenshot

Bandage

https://github.com/rrwick/Bandage/

Publication: (direct link) (doi link) (2015) (# citations 946)

Language: C++

Tags: Graph

Note: See also BandageNG https://github.com/asl/BandageNG

Github Stargazers: 448

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: 35

gGnomes

https://github.com/mskilab/gGnome

Language: R

Tags: SV, CNV, Breakends, Graph

Github Stargazers: 22

Platform: Web

gGnomes.js

https://github.com/mskilab/gGnome.js

Language: JS

Tags: SV, CNV, Breakends, Graph

Github Stargazers: 19

Platform: Web

graphgenomeviewer

https://cmdcolin.github.io/graphgenomeviewer/

Language: JS

Tags: Graph

Github: https://github.com/cmdcolin/graphgenomeviewer/

Github Stargazers: 4

Platform: Web

MoMi-G

https://github.com/MoMI-G/MoMI-G

Publication: (doi link) (2019) (# citations 13)

Language: JS

Tags: Graph, Multi, Alignment viewer, Circular, SV

Github Stargazers: 71

Platform: Web

odgi draw + odgi viz + odgi inject

https://odgi.readthedocs.io/en/latest/index.html

Publication: (doi link) (2021) (# citations 9)

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: 116

screenshot of odgi draw + odgi viz + odgi inject

sequence tube map

https://github.com/vgteam/sequenceTubeMap

Publication: (doi link) (2019) (# citations 18)

Language: JS

Tags: Graph

Github Stargazers: 118

Platform: Web

Alan

https://github.com/mpdunne/alan

Language: Bash

Tags: Text based, MSA

Github Stargazers: 73

Platform: CLI

Alv

https://github.com/arvestad/alv

Publication: (doi link) (2018) (# citations 2)

Language: Python

Tags: Text based, MSA

Github Stargazers: 74

Platform: CLI

ASCIIGenome

https://github.com/dariober/ASCIIGenome

Publication: (doi link) (2017) (# citations 1)

Language: Java

Tags: Text based, Alignment viewer

Github Stargazers: 181

Platform: CLI

Bamcov

https://github.com/fbreitwieser/bamcov

Language: C

Tags: Text based, Coverage

Github Stargazers: 89

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 9802)

Language: C++

Tags: Text based

Platform: CLI

No screenshot

Hapviz

https://github.com/ekg/hapviz

Language: C

Tags: Text based

Github Stargazers: 11

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 4)

Language: Python

Tags: Alignment 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

screenshot of Rna Alignment Viewers (Colorstock, SScolor, Ratón)

Sam2pairwise

https://github.com/mlafave/sam2pairwise

Publication: (doi link)

Language: C++

Tags: Text based

Github Stargazers: 28

Platform: CLI

No screenshot

Samtools depth visualization

https://twitter.com/yokofakun/status/1178686978541441025

Tags: Text based, Coverage

Platform: CLI, GNUplot

screenshot of Samtools depth visualization

Samtools tview

http://www.htslib.org/

Publication: (doi link) (2009) (# citations 35044)

Language: C

Tags: Text based, Alignment viewer

Github: https://github.com/samtools/samtools

Github Stargazers: 1226

Platform: CLI

SvABA

https://github.com/walaj/svaba#alignmentstxtgz

Publication: (doi link) (2018) (# citations 183)

Tags: Text based

Github Stargazers: 179

Platform: CLI

VizAln (from HipSTR)

https://github.com/tfwillems/HipSTR

Publication: (doi link) (2017) (# citations 133)

Tags: Text based

Github Stargazers: 74

Anvio

https://peerj.com/articles/1319/

Publication: (doi link) (2015) (# citations 961)

Language: Python

Tags: Circular

Github: https://github.com/merenlab/anvio

Github Stargazers: 346

No screenshot

BioCircos.js

http://bioinfo.ibp.ac.cn/biocircos/

Publication: (doi link) (2016) (# citations 76)

Language: JS

Tags: Circular

Platform: Web

Circa

https://omgenomics.com/circa

Tags: Commercial, Circular

Platform: Desktop

Circleator

http://jonathancrabtree.github.io/Circleator/index.html

Publication: (doi link) (2014) (# citations 24)

Language: Perl

Tags: Circular, Static

Github: https://github.com/jonathancrabtree/Circleator

Github Stargazers: 41

circlize

https://github.com/jokergoo/circlize

Publication: (doi link) (2014) (# citations 1511)

Language: R

Tags: Circular, Static

Github Stargazers: 797

Circos

http://circos.ca/

Publication: (doi link) (2009) (# citations 6405)

Language: Perl

Tags: Circular, Static

Note: the github repo is not up to date with the latest code

Github: https://github.com/vigsterkr/circos

Github Stargazers: 57

CircosJS

https://github.com/nicgirault/circosJS

Language: JS

Tags: Circular

Github Stargazers: 457

Platform: Web

DNAPlotter

https://www.sanger.ac.uk/science/tools/dnaplotter

Publication: (doi link) (2008) (# citations 609)

Language: Java

Tags: Circular

Platform: Desktop

GenomeProjector

https://github.com/gaou/g-language/wiki

Publication: (direct link) (doi link) (2009) (# citations 31)

Language: Perl

Tags: Circular, Linear

Github: https://github.com/gaou/g-language

Platform: Desktop

JupiterPlot

https://github.com/JustinChu/JupiterPlot

Publication: (doi link)

Language: Perl

Tags: Circular, Static, Comparative

Github Stargazers: 51

mummer2circos

https://github.com/metagenlab/mummer2circos

Language: Python

Tags: Static

Github Stargazers: 56

OGDRAW

https://chlorobox.mpimp-golm.mpg.de/OGDraw.html

Publication: (doi link) (2019) (# citations 501)

Tags: Circular, Static

Platform: Web

seqviz

https://github.com/Lattice-Automation/seqviz#viewer

Tags: Synthetic biology

Github Stargazers: 108

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://www.ncbi.nlm.nih.gov/pmc/articles/PMC151184/

Publication: (direct link) (doi link) (2002) (# citations 211)

Language: Java

Tags: Special-purpose, Historical, Deadlink?, Gene structure, Annotation, Comparative

Platform: Desktop

Apollo aka WebApollo

https://genomearchitect.readthedocs.io/en/latest/

Publication: (doi link) (2013) (# citations 282)

Language: Java, Groovy, JS

Tags: Gene structure, Annotation, JBrowse integration

Github: https://github.com/gmod/apollo

Github Stargazers: 105

Platform: Web

Chopchop

http://chopchop.cbu.uib.no/

Publication: (doi link) (2019) (# citations 521)

Tags: Synthetic biology

Chromatic

https://chromatic.nci.nih.gov/

Publication: (direct link) (doi link) (2018) (# citations 1)

Language: WASM

http://www.acsu.buffalo.edu/~lm69/cnvCurator

Platform: Web

cnvCurator

Publication: (direct link) (doi link) (2015) (# citations 1)

Language: Java

Tags: CNV, Annotation, Deadlink?

Platform: Desktop

D3GB

http://d3gb.usal.es/

Publication: (doi link) (2017) (# citations 6)

Language: JS, D3

https://www.dnaskittle.com/

Github: https://github.com/BioinfoUSAL/D3GB

Platform: Web

DNASkittle

Publication: (doi link) (2009) (# citations 6)

https://easeq.net/screenshots/

Github: https://github.com/josiahseaman/skittle

Github Stargazers: 5

Platform: Web

EaSeq

Publication: (direct link) (doi link) (2016) (# citations 153)

Tags: Special-purpose, Epigenomics

Platform: Desktop

FluentDNA

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7203487/

Publication: (doi link) (2020) (# citations 2)

http://labsergen.langebio.cinvestav.mx/bioinformatics/jacob/?p=473

Platform: Web

Gambit

Tags: Alignment viewer, Linear

Platform: Desktop

Ribbon

http://genomeribbon.com/

Publication: (direct link) (doi link) (2020) (# citations 17)

Language: JS

Tags: SV, Alignment viewer

Github: https://github.com/MariaNattestad/ribbon

Github Stargazers: 219

Platform: Web

GenomeSpy

https://genomespy.app/

Language: JS, WebGL

Tags: CNV, GWAS, Linear, MSA

Github: https://github.com/genome-spy/genome-spy

Github Stargazers: 97

Platform: Web

Genoverse

https://github.com/wtsi-web/Genoverse

Language: JS

Tags: General, Linear

Github Stargazers: 89

Platform: Web

Gnomad browser

https://github.com/macarthur-lab/gnomadjs

Publication: (doi link) (2020) (# citations 3046)

Language: JS

Tags: Special-purpose, Linear, Population

Twitter: https://twitter.com/gnomad_project

Github Stargazers: 61

Platform: Web, Silo

Gremlin

http://compbio.cs.brown.edu/projects/gremlin/

Publication: (doi link) (2010) (# citations 19)

Tags: SV, Linear

Platform: Web

GTEX Locus browser

https://gtexportal.org/home/locusBrowserPage/ACTN3

Publication: (doi link) (2020) (# citations 947)

Tags: Expression, Linear, LD

Platform: Web

GWAS catalog browser

https://www.ebi.ac.uk/gwas/variants/rs1558902

Publication: (doi link) (2018) (# citations 1898)

Tags: Population, LD, GWAS

Twitter: https://twitter.com/gwascatalog?lang=en

Platform: Web

Hawkeye

Publication: (direct link) (doi link) (2007) (# citations 54)

Language: C++

Tags: Special-purpose, Alignment 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 57)

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 69)

Tags: Assembly QC

Github: https://github.com/ablab/quast

Github Stargazers: 252

Platform: Web

InGAP-SV

http://ingap.sourceforge.net/

Publication: (doi link) (2011) (# citations 59)

Language: Java

Tags: SV, Alignment 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 241)

Language: JS, D3

http://bioinformatics.zj.cn/magicviewer/

Note: web app using it here https://pathogenomics.sfu.ca/islandviewer uses D3, SVG

Github: https://github.com/lairdm/islandplot

Github Stargazers: 32

Platform: Web

screenshot of IslandViewer and IslandPlot

MagicViewer

Publication: (direct link) (doi link) (2010) (# citations 39)

Tags: Special-purpose, Deadlink?

Platform: Desktop

Locuszoom

http://locuszoom.org/

Publication: (doi link) (2010) (# citations 1843)

Tags: GWAS, Population

Note: Also see locuszoom.js http://locuszoom.org/locuszoomjs.php

Github: https://github.com/statgen/locuszoom

Github Stargazers: 121

Platform: Web

LookSeq

https://www.sanger.ac.uk/tool/lookseq/

Publication: (doi link) (2009) (# citations 49)

https://www.malariagen.net/apps/ag1000g/phase1-AR3/index.html

Github: https://github.com/magnusmanske/lookseq

Github Stargazers: 4

Platform: Web

Panoptes

Publication: (doi link) (2017) (# citations 5)

Language: Python, JS

Tags: Special-purpose, Population

Github: https://github.com/cggh/panoptes

Github Stargazers: 36

MapView

https://sites.google.com/site/wjwdavy/

Publication: (direct link) (doi link) (2009) (# citations 64)

Tags: Special-purpose, Alignment viewer

Note: links in original paper are dead, but URL provided here works

Platform: Desktop

NGB

https://github.com/epam/NGB

Language: Java

Tags: Special-purpose, Alignment viewer

Github Stargazers: 133

Platform: Web

SeqCover

https://brentp.github.io/seqcover/#gene=AIFM1

Tags: Special-purpose, Coverage

Github: https://github.com/brentp/seqcover

Github Stargazers: 45

Platform: Web

SEQing

https://github.com/malewins/SEQing

Publication: (doi link) (2020) (# citations 4)

Language: Python

https://gene.sfari.org/database/human-gene/

Github Stargazers: 6

Platform: Web

SFARI

Publication: (doi link) (2010) (# citations 161)

Tags: Special-purpose, CNV

Platform: Web, Silo

Short read assembly browser

https://rapdb.dna.affrc.go.jp/AssemblyBrowser2/index.html?ref=%22chr01%22&run_id=%22G4toI1%22&start=%22234780%22&end=%22236631%22

Publication: (doi link) (2013) (# citations 429)

Tags: Special-purpose, Alignment viewer

Platform: Web, Silo

screenshot of Short read assembly browser

SNPitty

https://bitbucket.org/ccbc/snpitty/src/master/

Publication: (direct link) (doi link) (2018) (# citations 11)

Language: R

Tags: Special-purpose, CNV

Platform: Web

SNIPViz

http://www.yeastrc.org/snipviz/4.HTML_Config_retrieve_newick_and_fasta_from_server/snip_viz_HTML_config_with_newick_clustering.html

Publication: (doi link) (2014) (# citations 7)

Tags: MSA, Deadlink

Github: https://github.com/yeastrc/snipviz

Github Stargazers: 19

Platform: Web

SplitThreader

http://splitthreader.com/

Publication: (doi link) (2016) (# citations 10)

Language: JS, PHP

Tags: SV, CNV

Github: https://github.com/MariaNattestad/SplitThreader

Github Stargazers: 65

Platform: Web

Staden

https://sourceforge.net/projects/staden/

Publication: (doi link) (2010) (# citations 167)

Language: C, Tcl/Tk

Tags: Special-purpose, Alignment viewer, Assembly

Platform: Desktop

TASUKE

https://ricegenome.dna.affrc.go.jp/

Publication: (doi link) (2019) (# citations 12)

Tags: Special-purpose, Pangenome

Note: info about multi-genome-browser https://tasuke.dna.affrc.go.jp/

Platform: Web

TE-nest

Publication: (doi link) (2007) (# citations 54)

Tags: Special-purpose, Transposons, 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/

Platform: Web, CGI, Server

Transposcope

Publication: (doi link) (2020) (# citations 0)

Language: JS

Tags: Special-purpose, Transposons

Github: https://github.com/FenyoLab/transposcope

Github Stargazers: 5

Platform: Web

UGENE

http://ugene.net/

Publication: (doi link) (2012) (# citations 1395)

Language: C++

https://varsome.com/security-validation/?next=/variant/hg19/NM_000088.3(COL1A1):c.658C%3ET

Github: https://github.com/ugeneunipro/ugene

Github Stargazers: 150

Platform: Desktop

Varsome

Publication: (doi link) (2018) (# citations 618)

Tags: Special-purpose, Annotation

Platform: Web, Silo

Vials

http://vials.io/

Publication: (doi link) (2016) (# citations 13)

Tags: Special-purpose, Splicing

Github: https://github.com/Caleydo/vials

Github Stargazers: 13

Platform: Web

No screenshot

wasm bigwig demo browser

https://shk656461.github.io/index.html

Language: WASM

Tags: Special-purpose, Quantitative

Platform: Web

BasePlayer

https://baseplayer.fi/

Publication: (direct link) (doi link) (2018) (# citations 18)

Language: Java

Tags: General

Github: https://github.com/rkataine/BasePlayer

Github Stargazers: 4

Platform: Desktop

Celera genome browser

https://www.csee.umbc.edu/~turner/presentations/bvw2002/sld009.htm

Tags: General, Historical, Alignment viewer

Platform: Desktop

IGB

https://bioviz.org/

Publication: (direct link) (doi link) (2016) (# citations 232)

Language: Java

http://bioinformatics-ca.github.io/savant_genome_browser_lab_2015/

Platform: Desktop

IGV

https://igv.org/

Publication: (doi link) (2011) (# citations 8303)

Language: Java

Tags: General, Alignment viewer, SV, Quantitative

Github: https://github.com/igvteam/igv

Github Stargazers: 492

Platform: Desktop

Savant

Publication: (direct link) (doi link) (2012) (# citations 42)

Language: Java

Tags: General, SV, Alignment 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 634)

Language: Java

https://blog.dnanexus.com/2019-05-21-bigtop-data-visualization/

Github: https://github.com/cropgeeks/tablet

Github Stargazers: 29

Platform: Desktop

BigTop

Language: JS

Tags: Exotic, GWAS

Github: https://github.com/dnanexus/bigtop

Github Stargazers: 3

Platform: Web

Cylindrical alignment app

https://sourceforge.net/projects/cylindrical-alignment-app/

Alt url https://sourceforge.net/projects/cyl-viewer/

Tags: Exotic

Platform: Desktop

Biodalliance

http://www.biodalliance.org/

Publication: (doi link) (2011) (# citations 87)

Language: JS

https://useast.ensembl.org/Homo_sapiens/Location/View?r=17:63992802-64038237

Github: https://github.com/dasmoth/dalliance

Github Stargazers: 217

Platform: Web

Ensembl genome browser

Publication: (doi link) (2002) (# citations 1032)

Tags: General, Comparative

Platform: Web, Silo

Ensembl genome browser 2020 edition

http://2020.ensembl.org/

Tags: General, Comparative

Platform: Web

screenshot of Ensembl genome browser 2020 edition

GBrowse 2

http://gmod.org/wiki/GBrowse

Publication: (doi link) (2013) (# citations 95)

Language: Perl

Tags: General

Note: Original gbrowse paper https://doi.org/10.1101/gr.403602

Github: https://github.com/GMOD/GBrowse

Github Stargazers: 46

Platform: Web

GenomeMaps

http://www.genomemaps.org/

Publication: (direct link) (doi link) (2013) (# citations 22)

Language: JS

Tags: General, Deadlink

Github: https://github.com/opencb/genome-maps

Github Stargazers: 38

Gosling

https://gosling.js.org/

Publication: (doi link) (2022) (# citations 1)

Language: JS, WebGL, Typescript, React

Tags: General, Epigenomics, Higlass integration, Linear, Circular, Comparative, Quantitative

Github: https://github.com/gosling-lang/gosling.js

Github Stargazers: 97

Platform: Web

HiGlass

https://higlass.io

Publication: (doi link) (2018) (# citations 252)

Language: JS, WebGL

Tags: General, Epigenomics, Hi-C

Github: https://github.com/higlass/higlass

Github Stargazers: 242

Platform: Web, Server

IGV.js

https://github.com/igvteam/igv.js/

Publication: (doi link) (2020) (# citations 21)

Language: JS

http://jbrowse.org/jbrowse1.html

Github Stargazers: 513

Platform: Web

JBrowse

Publication: (doi link) (2016) (# citations 453)

Language: JS

Tags: General, Alignment 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: 429

Platform: Web, Desktop

JBrowse 2

http://jbrowse.org/jb2

Language: JS, Typescript, React

Tags: General, SV, Comparative, Dotplot, Circular, Alignment viewer, Quantitative, Hi-C

Note: See gallery for more examples https://jbrowse.org/jb2/gallery

Github: https://github.com/GMOD/jbrowse-components

Github Stargazers: 92

Platform: Web

Kero-BROWSE

https://kero.hgc.jp/examples/CLCL/hg38/index.html

Publication: (doi link) (2017) (# citations 32)

Language: JS

Tags: General, SV, Alignment 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: 6

Platform: Web

NCBI Genome Data Viewer

https://www.ncbi.nlm.nih.gov/genome/gdv/

Publication: (doi link) (2020) (# citations 21)

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

Tags: General, Multi

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 16)

Language: JS

Tags: General, SV

Github Stargazers: 262

Platform: Web

Trackster

https://galaxyproject.org/learn/visualization/

Publication: (doi link) (2012) (# citations 21)

Tags: General

Platform: Web

UCSC genome browser

https://genome.ucsc.edu/

Publication: (doi link) (2002) (# citations 4263)

Tags: General

Github: https://github.com/ucscGenomeBrowser/kent

Github Stargazers: 167

Platform: Web, Silo

Valis browser

https://valis.bio/

Language: JS, WebGL

Tags: General, Quantitative, Epigenomics, Deadlink

Github: https://github.com/VALIS-software/valis-hpgv

Github Stargazers: 12

Platform: Web

WashU epigenomics browser

https://epigenomegateway.wustl.edu/

Publication: (doi link) (2019) (# citations 136)

Language: JS, React

Tags: General, Epigenomics, Hi-C

Note: features redesign, there is also a legacy version

Github: https://github.com/lidaof/eg-react

Github Stargazers: 41

Platform: Web

Zenbu

http://fantom.gsc.riken.jp/zenbu/

Publication: (doi link) (2014) (# citations 130)

Tags: General

Platform: Web

cgplot

https://github.com/dfguan/cgplot

Language: Python

Tags: Static, Dotplot, Comparative

Github Stargazers: 7

D-GENIES

http://dgenies.toulouse.inra.fr/

Publication: (doi link) (2018) (# citations 213)

Language: JS, Python, D3

Tags: Dotplot, Comparative

Github: https://github.com/genotoul-bioinfo/dgenies

Github Stargazers: 73

Platform: Web

Delly-maze

https://github.com/dellytools/maze

Publication: (doi link) (2012) (# citations 1254)

Language: Python

https://github.com/mjsull/DiscoPlot

Note: see also https://www.gear-genomics.com/maze/

Github Stargazers: 9

Discoplot

Publication: (doi link) (2015) (# citations 0)

Language: Python

https://dotlet.vital-it.ch/

Github Stargazers: 9

Dot

https://dot.sandbox.bio/

Language: JS, Python

Tags: Dotplot, Comparative

Note: Python data preparation script

Github: https://github.com/MariaNattestad/dot

Github Stargazers: 17

Platform: Web

Dotlet

Publication: (doi link) (2000) (# citations 73)

Language: JS, React

Tags: Dotplot

Note: The original publication was 2000 but updated ~2020 with reactjs

Github: https://github.com/sib-swiss/dotlet

Github Stargazers: 2

Platform: Web

Dotplot (chirimoyo)

https://chirimoyo.ac.uma.es/bitlab/portfolio/dotplot/

Tags: Dotplot, Deadlink?

Platform: Web

No screenshot

iLambda/Dotplot

https://github.com/iLambda/dotplot

Tags: Dotplot

Github Stargazers: 1

Platform: Web

No screenshot

dotPlotly

https://github.com/tpoorten/dotPlotly/

Language: R, Shiny

Tags: Dotplot, Comparative

Github Stargazers: 128

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 36)

Language: Python

Tags: Dotplot

Github Stargazers: 72

Platform: CLI

Gepard

http://cube.univie.ac.at/gepard

Publication: (doi link) (2007) (# citations 485)

Language: Java

Tags: Dotplot, Comparative

Github: https://github.com/univieCUBE/gepard

Github Stargazers: 36

Platform: Desktop

Jdot

https://github.com/LyonsLab/jdot

Language: JS

Tags: Dotplot, Comparative

Github Stargazers: 1

Platform: Web

last-dotplot

https://gitlab.com/mcfrith/last

Language: Python, C++

Tags: Dotplot, Comparative

Platform: CLI, Web-server

mcutils

https://github.com/mchaisso/mcutils

Language: R, C++

https://github.com/thackl/minidot

Note: https://twitter.com/mjpchaisson/status/1040363992206569472

Github Stargazers: 12

Minidot

Language: R

https://github.com/ryought/mummer-idotplot

Github Stargazers: 62

Mummer-idotplot

Language: JS, Python

Tags: Dotplot, Comparative

Github Stargazers: 21

Platform: Web, CLI

No screenshot

Mummerplot

http://mummer.sourceforge.net/

Publication: (doi link) (2004) (# citations 3704)

Language: GNUPlot

https://jmonlong.github.io/Hippocamplus/2017/09/19/mummerplots-with-ggplot2/

Github: https://github.com/mummer4/mummer

Github Stargazers: 309

ggplot2 mummerplot

Language: R

Tags: Dotplot, Comparative

Redotable

https://github.com/s-andrews/redotable

Language: Java

Tags: Dotplot, Comparative

Github Stargazers: 8

Platform: Desktop

syntenyPlotByR

https://github.com/shingocat/syntenyPlotByR

Language: R

Tags: Dotplot, Comparative, Static

Github Stargazers: 7

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

https://chipster.csc.fi/

Publication: (doi link) (2011) (# citations 239)

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: 34

Platform: Desktop

cisGenome Browser

https://jhui2014.github.io/browser/screenshots.html

Publication: (doi link) (2010) (# citations 32)

Language: C

Tags: Epigenomics

Platform: Desktop

Epilogos

https://epilogos.altius.org/

Language: Python

Tags: Epigenomics, Higlass integration

Github: https://github.com/meuleman/epilogos

Github Stargazers: 33

Platform: Web

Epiviz

https://epiviz.github.io/

Publication: (doi link) (2020) (# citations 1)

Language: JS, R, D3

Tags: Epigenomics

Github: https://github.com/epiviz/epiviz

Github Stargazers: 66

Platform: Web

HiPiler

http://hipiler.higlass.io

Publication: (doi link) (2018) (# citations 27)

Language: JS

Tags: Epigenomics, Hi-C, Higlass integration

Github: https://github.com/flekschas/hipiler

Github Stargazers: 11

Platform: Web

Juicebox

https://github.com/aidenlab/Juicebox

Publication: (direct link) (doi link) (2016) (# citations 688)

Language: Java

Tags: Epigenomics, Hi-C

Github Stargazers: 167

Platform: Desktop

Juicebox.js

http://www.igv.org/doc/juiceboxjs.html

Publication: (direct link) (doi link) (2018) (# citations 139)

Language: JS

Tags: Epigenomics, Hi-C

Github: https://github.com/igvteam/juicebox.js

Github Stargazers: 15

Platform: Web

Peax

https://github.com/Novartis/peax

Publication: (doi link) (2020) (# citations 7)

Language: JS

Tags: Epigenomics, Higlass integration

Github Stargazers: 61

Platform: Web

eweitz/Ideogram

https://github.com/eweitz/ideogram

Language: JS

Tags: Ideogram

Github Stargazers: 228

Platform: Web

Ideogram

https://github.com/RCollins13/HumanIdiogramLibrary

Publication: (doi link)

Language: SVG

Tags: Ideogram, Static

Github Stargazers: 76

Ideoplot

https://github.com/mchaisso/Ideoplot

Language: R

Tags: Ideogram, Static

Github Stargazers: 12

No screenshot

karyoploteR

https://github.com/bernatgel/karyoploteR

Publication: (doi link) (2017) (# citations 299)

Language: R

Tags: Ideogram, Static

Github Stargazers: 232

KaryotypeSVG

https://github.com/andreasprlic/karyotypeSVG

Language: JS, SVG

Tags: Ideogram

Github Stargazers: 5

Platform: Web

NCBI Genome Decoration

https://www.ncbi.nlm.nih.gov/genome/tools/gdp/

Tags: Ideogram

Platform: Web, Form, Silo

UCSC Genome Graphs

http://genome.ucsc.edu/cgi-bin/hgGenome

Publication: (doi link) (2002) (# citations 4263)

Tags: Ideogram

Github: https://github.com/ucscGenomeBrowser/kent

Github Stargazers: 167

Platform: Web, Form, Silo

iGenomics

Publication: (doi link) (2020) (# citations 10)

Language: Objective-C

Tags: Mobile, Alignment viewer

Github: https://github.com/stuckinaboot/iGenomics

Github Stargazers: 33

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 8)

Tags: Pangenome

Github Stargazers: 6

Panache

https://github.com/SouthGreenPlatform/panache

Publication: (doi link) (2021) (# citations 4)

Language: JS, VueJS

Tags: Pangenome

Github Stargazers: 32

panX

http://pangenome.tuebingen.mpg.de/

Publication: (direct link) (doi link) (2017) (# citations 136)

Tags: Pangenome, Deadlink?

Github: https://github.com/neherlab/pan-genome-analysis

Github Stargazers: 103

RPAN (3kricedb)

http://cgm.sjtu.edu.cn/3kricedb/visualization/?tracks=DNA%2Cgene%2CPF

Publication: (doi link) (2016) (# citations 80)

Tags: Pangenome, JBrowse integration

Platform: Web

Protael

http://sanshu.github.io/protaelweb/

Publication: (direct link) (doi link) (2015) (# citations 8)

Language: JS

Tags: Protein, MSA

Github: https://github.com/sanshu/protaeljs

Github Stargazers: 18

Platform: Web

ProteinPaint

https://pecan.stjude.cloud/proteinpaint

Publication: (direct link) (doi link) (2015) (# citations 173)

Tags: Protein, Cancer, Lollipops

Note: Not open source

Platform: Web

GenomePaint

https://genomepaint.stjude.cloud/

Publication: (direct link) (doi link) (2021) (# citations 9)

Tags: CNV, Linear, Cancer, Lollipops

Note: Not open source

Platform: Web

pViz

https://github.com/Genentech/pviz

Publication: (doi link) (2014) (# citations 18)

Language: JS

Tags: Protein

Github Stargazers: 62

Platform: Web

UCSC Xena

https://xena.ucsc.edu/

Publication: (doi link) (2020) (# citations 802)

Language: JS

Tags: Heatmap, Population

Github: https://github.com/ucscXena/ucsc-xena-client

Github Stargazers: 49

Platform: Web

VIVA

https://www.biorxiv.org/content/10.1101/589879v1.full.pdf

Publication: (doi link) (2019) (# citations 3)

Tags: Heatmap, Population, Variants

Github: https://github.com/compbiocore/VariantVisualization.jl

Github Stargazers: 58

Platform: Web

Dotter

https://sonnhammer.sbc.su.se/Dotter.html

Publication: (doi link) (1995) (# citations 444)

Tags: Dotplot

Platform: CLI

REPAVER

https://gitlab.com/gringer/bioinfscripts/

Publication: (direct link) (doi link)

Language: R, C++

Tags: Repeats, Dotplot, Static, Linear

Platform: CLI

LinearDisplay.pl

https://github.com/JCVenterInstitute/LinearDisplay

Publication: (doi link) (2019) (# citations 273)

Language: Perl

Tags: Comparative

Note: readme says to cite this paper

Github Stargazers: 2

Platform: CLI

Gview

https://server.gview.ca/examples

Publication: (doi link) (2010) (# citations 222)

Language: Perl, Java, Java web start

Tags: Circular, Linear, Pangenome, Microbiology

Platform: Web

FastANI

https://github.com/ParBLiSS/FastANI

Publication: (doi link) (2018) (# citations 1235)

Language: C++

Tags: Comparative, Microbiology

Github Stargazers: 237

JGI/IMG

https://img.jgi.doe.gov/

Tags: Dotplot, Linear, Microbiology

Note: Dotplot use MUMmer

Platform: Web, Silo

covviz

https://brwnj.github.io/covviz/

Language: JS

Tags: CNV, Coverage, Population

Github: https://github.com/brwnj/covviz

Github Stargazers: 45

clinker

https://github.com/gamcil/clinker

Publication: (direct link) (doi link) (2021) (# citations 123)

Language: JS

Tags: Comparative, Gene order

Github Stargazers: 350

Platform: Web

PopSV

https://github.com/jmonlong/PopSV/blob/master/3-Visualization.md

Publication: (doi link) (2018) (# citations 30)

Language: R

Tags: Population, SV

Github: https://github.com/jmonlong/PopSV

Github Stargazers: 25

Platform: Web

Shasta

https://chanzuckerberg.github.io/shasta/ComputationalMethods.html#ReadGraph

Publication: (doi link) (2020) (# citations 185)

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 24)

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: 109

PURPLE

https://github.com/hartwigmedical/hmftools/blob/master/purity-ploidy-estimator/README.md

Publication: (doi link) (2019) (# citations 24)

Tags: CNV, Cancer

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: 109

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: 101

sockeye

https://www.bcgsc.ca/resources/software/sockeye

Publication: (direct link) (doi link) (2004) (# citations 20)

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 320)

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: 469

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: 469

mocha

https://github.com/freeseek/mocha

Publication: (doi link) (2018) (# citations 166)

Language: C, WDL, R

Tags: CNV

Note: Has a full analysis pipeline associated with end result visualizations

Github Stargazers: 54

ALVIS (MSA viewer)

https://www.ebi.ac.uk/research/goldman/software/alvis

Publication: (direct link) (doi link) (2016) (# citations 8)

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 5)

Language: Java

Tags: QC, Assembly

Github Stargazers: 14

screenshot of ALVIS (chimeric alignment viewer)

genevisR

https://bioconductor.org/packages/release/bioc/vignettes/GenVisR/inst/doc/Intro.html

Publication: (doi link) (2016) (# citations 163)

Language: R

Tags: CNV

Github: https://github.com/griffithlab/GenVisR

Github Stargazers: 185

NanoMethViz

http://www.bioconductor.org/packages/release/bioc/html/NanoMethViz.html

Publication: (doi link) (2021) (# citations 2)

Language: R

Tags: Methylation

Github: https://github.com/Shians/NanoMethViz

Github Stargazers: 7

GfaViz

Publication: (direct link) (doi link) (2018) (# citations 11)

Language: C++

Tags: Graph

Github: https://github.com/ggonnella/gfaviz

Github Stargazers: 43

Nextclade

https://clades.nextstrain.org/

Publication: (doi link) (2021) (# citations 103)

Language: JS, React, D3

Tags: Phylogenetics, Microbiology

Note: Related usage on nextstrain app also

vcfR

https://knausb.github.io/vcfR_documentation/

Publication: (doi link) (2016) (# citations 373)

Language: R

Tags: QC, Population, Coverage

Note: image shows chromoqc output

Github: https://github.com/knausb/vcfR

Github Stargazers: 191

asgart

Publication: (direct link) (doi link) (2018) (# citations 5)

Language: Rust

Tags: SV, Ideogram, Circular, Linear

Github: https://github.com/delehef/asgart

Github Stargazers: 13

MashMap

https://github.com/marbl/MashMap/blob/master/scripts/generateDotPlot

Publication: (doi link) (2018) (# citations 67)

Language: Perl, C++

Tags: Dotplot

Github: https://github.com/marbl/MashMap

Github Stargazers: 184

udon

https://github.com/ocxtal/udon

Language: Rust

https://brainome.ucsd.edu/howto_annoj.html

Note: Uses an advanced data structure for pileup, so visually a basic example but likely just a small demo

Github Stargazers: 12

AnnoJ

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 3)

Language: Python

Tags: Long reads, Methylation

Github Stargazers: 53

SWAV

http://swav.popgenetics.net/

Publication: (direct link) (doi link) (2020) (# citations 4)

Tags: Population, Deadlink

gingko

http://qb.cshl.edu/ginkgo/?q=/9EiUttUP0CBHs3WnuBa0

Publication: (doi link) (2015) (# citations 163)

Language: PHP, JS

Tags: Single cell, CNV

Github: https://github.com/robertaboukhalil/ginkgo

Github Stargazers: 42

Platform: Web

copynumber

https://www.bioconductor.org/packages/release/bioc/vignettes/copynumber/inst/doc/copynumber.pdf

Publication: (doi link) (2012) (# citations 193)

Language: R

Tags: CNV

alignfigR

https://cran.r-project.org/web/packages/alignfigR/vignettes/my-vignette.html

Language: R

Tags: MSA

copykat

https://github.com/navinlabcode/copykat/blob/master/vignettes/copycat-vignettes.pdf

Publication: (doi link) (2021) (# citations 75)

Language: R

Tags: Single cell, CNV

Github: https://github.com/navinlabcode/copykat

Github Stargazers: 113

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 43)

Language: R

Tags: Single cell, CNV

Github Stargazers: 58

RectChr

https://github.com/BGI-shenzhen/RectChr

Language: Binary blob, Perl

Tags: Comparative, Ideogram, Static, Limited code available

Github Stargazers: 49

LDBlockShow

https://github.com/BGI-shenzhen/LDBlockShow

Publication: (direct link) (doi link) (2020) (# citations 41)

Language: C++, Perl

Tags: GWAS, Population

Github Stargazers: 75

clinker (gene fusion software)

https://github.com/Oshlack/Clinker/

Publication: (direct link) (doi link) (2018) (# citations 11)

Language: R

Tags: Gene fusion

Github Stargazers: 43

screenshot of clinker (gene fusion software)

arriba

https://github.com/suhrig/arriba

Publication: (direct link) (doi link) (2021) (# citations 63)

Language: C++, R

Tags: Gene fusion

Github Stargazers: 150

FusionInspector

https://github.com/FusionInspector/FusionInspector/wiki

Publication: (doi link) (2021) (# citations 0)

Language: Perl, JS

Tags: Gene fusion

Note: Uses igv.js

Github: https://github.com/FusionInspector/FusionInspector

Github Stargazers: 36

NeoLoopFinder

https://github.com/XiaoTaoWang/NeoLoopFinder

Publication: (doi link) (2021) (# citations 13)

Language: Python

Tags: SV, Hi-C

Github Stargazers: 28

alen

https://github.com/jakobnissen/alen

Language: Rust

Tags: MSA, Text based

Github Stargazers: 46

Aquaria

http://aquaria.ws/Q9HD67/5i0i/A

Publication: (doi link) (2015) (# citations 50)

Tags: Protein, MSA

Platform: Web

vega

http://vega.archive.ensembl.org/Homo_sapiens/Location/Chromosome?r=6-QBL

Publication: (doi link) (2004) (# citations 89)

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 42)

Language: JS, Typescript

Tags: Protein, MSA

Note: Used on InterProScan website https://www.ebi.ac.uk/interpro/

Github: https://github.com/ebi-webcomponents/nightingale

Github Stargazers: 80

Platform: Web

ArchR

https://www.archrproject.com/articles/Articles/tutorial.html

Publication: (doi link) (2021) (# citations 191)

Language: R

Tags: Single cell

Github: https://github.com/GreenleafLab/ArchR

Github Stargazers: 235

PGAP-X

https://pgapx.zhaopage.com/

Publication: (direct link) (doi link) (2018) (# citations 17)

Language: C++

Tags: Pangenome

Platform: Desktop

MAVIS

http://mavis.bcgsc.ca/

Publication: (doi link) (2018) (# citations 15)

Language: Python

Tags: Gene fusion, SV

Github: https://github.com/bcgsc/mavis

Github Stargazers: 60

ProViz

http://slim.icr.ac.uk/proviz/index.php

Publication: (direct link) (doi link) (2016) (# citations 53)

Language: JS

Tags: MSA, Protein

Note: See also alphafold visualization as tracks http://slim.icr.ac.uk/projects/alphafold?page=alphafold_proviz_homepage

panGraphViewer

https://github.com/TF-Chan-Lab/panGraphViewer

Language: Python

Tags: Graph, Pangenome

Github Stargazers: 14

SVPV

https://github.com/VCCRI/SVPV

Publication: (direct link) (doi link) (2017) (# citations 7)

Language: Python

Tags: SV, Coverage

Github Stargazers: 28

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: 28

pretzel

https://github.com/plantinformatics/pretzel

Publication: (doi link) (2019) (# citations 16)

Language: JS, D3

Tags: Comparative, Genetic map

Github Stargazers: 29

splicejam

https://github.com/jmw86069/splicejam

Publication: (doi link) (2019) (# citations 25)

Language: R

Tags: Splicing, Sashimi

Github Stargazers: 20

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

Flash Gviewer

http://gmod.org/wiki/Flashgviewer/

Language: Flash, ActionScript

Tags: Ideogram, Genetic Map, Historical

Plotgardener

https://github.com/PhanstielLab/plotgardener/

Publication: (doi link) (2022) (# citations 3)

Language: R

Tags: Hi-C, Coverage

Github Stargazers: 191

MIRA

http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html

Publication: (doi link) (2004) (# citations 829)

Language: C++

Tags: Assembly, Alignment 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

Language: R, Perl

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: 7

IGGE

https://github.com/immersivegraphgenomeexplorer/IGGE

Publication: (doi link) (2021) (# citations 2)

Tags: Graph, Exotic

Note: Not open source

Github Stargazers: 1

PipMaker

http://pipmaker.bx.psu.edu/pipmaker/

Publication: (doi link) (2000) (# citations 849)

Tags: Comparative, Repeat, 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: 28

MEGA-X

https://www.megasoftware.net/

Publication: (doi link) (2021) (# citations 618)

Tags: MSA, Phylogenetics

Note: original paper from 1994 but actively updated. requires EULA for download

Platform: Desktop

Haploview

https://www.broadinstitute.org/haploview/haploview

Publication: (doi link) (2004) (# citations 10907)

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 18)

Language: Python

Tags: Comparative, Dotplot, Circular

Github Stargazers: 46

AmpliconArchitect

https://github.com/virajbdeshpande/AmpliconArchitect

Publication: (doi link) (2019) (# citations 74)

Language: Python

Tags: SV, Cancer

Note: The term amplicon refers essentially to extrachromosomal DNA in cancer

Github Stargazers: 87

PGV

https://github.com/ucrbioinfo/PGV

Publication: (direct link) (doi link) (2021) (# citations 1)

Language: Python

Tags: Pangenome, Dotplot, Comparative

Github Stargazers: 14

Platform: Web

REViewer

https://github.com/Illumina/REViewer

Publication: (direct link) (doi link) (2021) (# citations 1)

Tags: Repeats

Note: See also GraphAlignmentViewer, similar look and from illumina also

Github Stargazers: 43

Trackplot

https://github.com/PoisonAlien/trackplot

Publication: (doi link) (2014) (# citations 141)

Language: R

Tags: Coverage, Gene structure

Note: suggests citing bwtool linked here

Github Stargazers: 55

gcMapExplorer

https://github.com/rjdkmr/gcMapExplorer

Publication: (doi link) (2017) (# citations 18)

Language: Python

Tags: Hi-C

Github Stargazers: 16

BRIG

http://brig.sourceforge.net

Publication: (direct link) (doi link) (2011) (# citations 1737)

Language: Java

Tags: Comparative, Circular

Github: https://github.com/happykhan/BRIG

Github Stargazers: 13

Platform: Desktop

Ideogram viewer

https://bioinformatics.mdanderson.org/public-software/ideogramviewer/

Language: JS

Tags: Ideogram

Platform: Web

GENESPACE

https://github.com/jtlovell/GENESPACE/

Language: R

Tags: Comparative

Github Stargazers: 62

ggplot2 manhattan plot

https://danielroelfs.com/blog/how-i-create-manhattan-plots-using-ggplot/

Language: R, ggplot2

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 1099)

Language: Python

Tags: MSA, Phylogenetics

Github: https://github.com/etetoolkit/ete

Github Stargazers: 632

ggtree

https://github.com/YuLab-SMU/ggtree

Publication: (doi link) (2016) (# citations 1699)

Language: R

Tags: MSA, Phylogenetics, ggplot2

Note: see https://yulab-smu.top/treedata-book/chapter7.html?q=msa#msaplot for MSA example

Github Stargazers: 644

Phandango

https://jameshadfield.github.io/phandango/#/examples

Publication: (doi link) (2017) (# citations 258)

Language: JS

Tags: Pangenome, GWAS, MSA, Phylogenetics, Microbiology

Github: https://github.com/jameshadfield/phandango

Github Stargazers: 82

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

Tags: Circular, Cancer, SV

Github: https://github.com/cancerregulome/RegulomeExplorer

Github Stargazers: 4

Platform: Web

CGView

http://cgview.ca/

Publication: (doi link) (2008) (# citations 742)

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: 24

Platform: Web

miropeats

http://www.littlest.co.uk/software/bioinf/old_packages/miropeats/

Publication: (direct link) (doi link) (1995) (# citations 29)

Language: Perl, C

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 1)

Language: Python

Tags: Splicing, Coverage

Note: See also, clinker (gene fusion software)

Github Stargazers: 12

syntenyPlotteR

https://github.com/marta-fb/syntenyPlotteR

Language: R, ggplot2

Tags: Comparative

Github Stargazers: 14

chromoMap

https://lakshay-anand.github.io/chromoMap/index.html

Publication: (direct link) (doi link) (2022) (# citations 6)

Language: R