awesome-jbrowse2

awesome-jbrowse2

This is a companion website for the github repo https://github.com/cmdcolin/awesome-jbrowse2

Also check out our twitter account @awesomejbrowse2

Feel free to submit PRs to add more jbrowse 2 stuff!

Arabidopsis browser with nascent RNA sequencing data

https://zhailab-sustech.github.io/jbrowse2/

Publication:

Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing

(2021) (# citations 15)

screenshot of Arabidopsis browser with nascent RNA sequencing data

Japanese rhinoceros beetle browser

http://www.insect.nibb.info/trydi/jb/

Publication:

The draft genome sequence of Japanese rhinoceros beetle Trypoxylus dichotomus

(2022) (# citations 1)

screenshot of Japanese rhinoceros beetle browser

Atlantic chub mackerel browser

http://portugalfishomics.ciimar.up.pt/app/scombercolias/

Publication:

A genome assembly of the Atlantic chub mackerel (Scomber colias): a valuable teleost fishing resource

(2022) (# citations 3)

screenshot of Atlantic chub mackerel browser

Arabidopsis transposon discovery with Nanotei pipeline

Publication:

Transposons Hidden in Arabidopsis thaliana Genome Assembly Gaps and Mobilization of Non-Autonomous LTR Retrotransposons Unravelled by Nanotei Pipeline

(2021) (# citations 9)

screenshot of Arabidopsis transposon discovery with Nanotei pipeline

Serratus - Petabase scale viral discovery

https://www.serratus.io/jbrowse?bam=ERR2756788

Publication:

Petabase-scale sequence alignment catalyses viral discovery

(2022) (# citations 230)

screenshot of Serratus - Petabase scale viral discovery

TCMPG - Traditional Chinese medicinal plant genome database

http://cbcb.cdutcm.edu.cn/TCMPG/

Publication:

TCMPG: an integrative database for traditional Chinese medicine plant genomes

(2022) (# citations 17)

screenshot of TCMPG - Traditional Chinese medicinal plant genome database

S. pombe to cavanine (PomBase)

https://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Click%20on%20image%20to%20zoom&p=PMC3&id=8922049_25789430-2022-micropub.biology.000538.jpg

Publication:

Canavanine resistance mutation can1-1 in Schizosaccharomyces pombe is a missense mutation in the ubiquitin ligase adaptor gene any1

screenshot of S. pombe to cavanine (PomBase)

Black carpenter ant genome assembly

Publication:

De novosequencing, diploid assembly, and annotation of the black carpenter ant,Camponotus pennsylvanicus, and its symbionts by one person for $1000, using nanopore sequencing

(2022) (# citations 17)

screenshot of Black carpenter ant genome assembly

Methylation profiling in cereal crops

Publication:

Searching for a Needle in a Haystack: Cas9-Targeted Nanopore Sequencing and DNA Methylation Profiling of Full-Length Glutenin Genes in a Big Cereal Genome

(2021) (# citations 8)

screenshot of Methylation profiling in cereal crops

PhaeoEpiView - Diatom epigenome browser

Publication:

PhaeoEpiView: An epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum

(2022) (# citations 1)

screenshot of PhaeoEpiView - Diatom epigenome browser

Squalomix - shark and ray comparative genomics

Publication:

Squalomix: shark and ray genome analysis consortium and its data sharing platform

(2022) (# citations 13)

screenshot of Squalomix - shark and ray comparative genomics

FishSCT: zebrafish centric single-cell transcriptome database

Publication:

FishSCT: a zebrafish-centric database for exploration and visualization of fish single-cell transcriptome

(2022) (# citations 0)

screenshot of FishSCT: zebrafish centric single-cell transcriptome database

IAnimal: a cross-species omics knowledgebase for animals

Publication:

IAnimal: a cross-species omics knowledgebase for animals

(2022) (# citations 7)

screenshot of IAnimal: a cross-species omics knowledgebase for animals

GWAS Central

Publication:

GWAS Central: an expanding resource for finding and visualising genotype and phenotype data from genome-wide association studies

(2022) (# citations 15)

screenshot of GWAS Central

The Treenome Browser

Publication:

Treenome Browser: co-visualization of enormous phylogenies and millions of genomes

(2022) (# citations 5)

screenshot of The Treenome Browser