GitHub

A list of cool jbrowse stuff and links around the web

See also, awesome-jbrowse2 :) https://github.com/cmdcolin/awesome-jbrowse2

Main links

Homepage http://jbrowse.org/
JBrowse Configuration Guide - http://gmod.org/wiki/JBrowse_Configuration_Guide
JBrowse tutorial - http://jbrowse.org/code/latest-release/docs/tutorial
JBrowse FAQ - http://gmod.org/wiki/JBrowse_FAQ

Tutorials

Model organism databases

XenBase http://www.xenbase.org/entry/ (instance http://www.xenbase.org/common/displayJBrowse.do?data=data/xl9_1)
Rat Genome Database https://rgd.mcw.edu/ (instance https://rgd.mcw.edu/jbrowse/)
Mouse Genome Database http://www.informatics.jax.org/ (instance http://jbrowse.informatics.jax.org/?data=data/mouse)
WormBase http://www.wormbase.org (instance http://www.wormbase.org/tools/genome/jbrowse-simple/?data=data/c_elegans_PRJNA13758)
Yeast Genome Database - http://yeastgenome.org (instance https://browse.yeastgenome.org/)
Candida albicans - http://www.candidagenome.org/ (instance)
Dictybase - http://www.dictybase.org (instance)
Aspgd aspergillus http://aspgd.org (instance)
FlyBase http://flybase.org (instance http://flybase.org/jbrowse/?data=data/json/dmel)
PomBase https://www.pombase.org/ (instance https://www.pombase.org/jbrowse)

Topic databases

RepetDB - http://urgi.versailles.inra.fr/repetdb (2019 pub https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-019-0150-y)
IsoDB - PacBio Iso-Seq collection multiple species http://isodb.xieslab.org/ (2018 pub https://www.hindawi.com/journals/ijg/2018/9207637/cta/)
Nucleosome dynamics (yeast, mouse, human) http://mmb.irbbarcelona.org/NucleosomeDynamics/browse.php (example http://mmb.irbbarcelona.org/NucleosomeDynamics/JBrowse/JBrowse-1.11.6/index.html?data=user_jbrowse%2FR64-1-1%2Fjbrowse&loc=chrI%3A1..64&tracks=DNA%2CSGD_genes%2CGene_fromTSStoTTS&highlight=)
ApaDB (alternative polyadenylation) human, mouse chicken http://tools.genxpro.net/apadb/ (2014 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105710/)
ReproGenomicsViewer (RGV) http://rgv.genouest.org/ (example instance http://rgv.genouest.org/jbrowse/?data=sample_data%2Fjson%2FHuman%2Fhg19%2F&loc=chr1%3A99685667..149535791&tracks=DNA&highlight=)
YeasTSS - yeast transcription start sites http://www.yeastss.org/ (2018 pub https://www.biorxiv.org/content/early/2019/01/03/511477)
the database for imperfect interspersed mtDNA repeats annotation http://bioinfodbs.kantiana.ru/ImtRDB/ (2019 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6614062/)
ENdb - Human and mouse enhancer http://www.licpathway.net/ENdb/ (2019 pub https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz973/5608998)
tRFExplorer (tRNA derived ncRNAs) https://trfexplorer.cloud/ (2019 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6859256/)
ChipSummitDB - http://summit.med.unideb.hu/summitdb/ (2020 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6964213/)
Yeast histone http://geneart.med.unideb.hu/jbrowse/ (2020 pub, requires login see paper for login https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6970188/)
Structurome https://structurome.bb.iastate.edu/ (2020 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7263510/ https://structurome.bb.iastate.edu/jbrowse/)
Transposons (TRAdis-vault) https://qfab.org/biodata/high-performance-computing
MethBank https://bigd.big.ac.cn/methbank/jbrowse

Human

GWAS browser http://gwas-browser.nygenome.org
COSMIC browser http://cancer.sanger.ac.uk/cosmic (instance http://cancer.sanger.ac.uk/jbrowse/index.html?tracks=cosmic_genes,muts&dsn=cosmic&loc=17:7668510..7677703&data=data/json/grch38/v84/gene&genome=38)
Type1 Diabetes/ImmunoBase http://t1dbase.org/ (instance http://t1dbase.org/jbrowse/index.html)
PopHuman http://pophuman.uab.cat/ (2017 pub https://academic.oup.com/nar/article/46/D1/D1003/4559406)
Delta browser HiC http://delta.big.ac.cn/ (2017 pub https://www.biorxiv.org/content/early/2017/10/08/199950)
CAPER proteome http://www.bprc.ac.cn/CAPE
Swiss Regulon http://swissregulon.unibas.ch/sr/annotations
Neandertal genome browser https://bioinf.eva.mpg.de/jbrowse/?loc=1%3A99685667..149535791&tracks=&highlight= (paper http://science.sciencemag.org/content/358/6363/655)
Dasman http://dgr.dasmaninstitute.org/DGR/index.html (instance http://dgr.dasmaninstitute.org/JBrowse-1.12.3/index.html?loc=chr1%3A63064986..63065195&tracks=DNA&data=data%2F)
HumCFS (chromosome fragile sites) http://webs.iiitd.edu.in/raghava/humcfs/genome.php
Database of autozygous segments http://pembertonlab.med.umanitoba.ca/das.php (pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5709839/)
NIAGADS Alzheimers https://www.niagads.org/genomics/jbrowse.jsp
iHMS histone modification http://www.tongjidmb.com/human/index.html
RNAex (secondary structure prediction) http://lulab.life.tsinghua.edu.cn/RNAex/jbrowse.php?Species=S.cerevisiae&Build=SacCer2&Datatype=PARS&Location=
RNAstructureomeDB https://structurome.bb.iastate.edu/
Trident (St Jude Hospital) multi species http://trident.stjude.org/static/dre/
CCSI (chromatin conformation space interaction) http://120.79.23.67/ccsi/search.php
Neuroseq http://neuroseq.janelia.org/ (instance http://neuroseq.janelia.org/jbrowse/?data=data)
iMETHYL http://imethyl.iwate-megabank.org/genomebrowser.html
MeT-DB Methyltranscriptome http://compgenomics.utsa.edu/MeTDB/
EpiDeNovo http://www.epidenovo.biols.ac.cn/ (instance http://61.148.58.210:8080/EpiDenovo/JBrowse/index.html?data=hsa) (github https://github.com/rapsoulhaonan/EpiDenovo)
INDEXdb (Indian Exome DB) http://indexdb.ncbs.res.in/jbrowse/
Super enhancer DB seDB - http://www.licpathway.net/sedb/ (2018 pub https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky1025/5146197)
Database of somatic mutations in normal cells - http://dsmnc.big.ac.cn/ (2018 pub https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky1045/5150232)
BreCanDB - breakpoints in cancer http://brecandb.igib.res.in/ (2015 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702892/)
Japanese genome JG1 https://jmorp.megabank.tohoku.ac.jp
RNAMod - https://bioinformatics.sc.cn/RNAmod/ (2019 pub https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz479/5506862)
HGVD - https://www.hgvd.genome.med.kyoto-u.ac.jp/pub/jbrowse_index.html?loc=chr9&tracks=DNA%2CGenes%2Cfrequency_org_all%2Cfreq_org_count_allcall%2Cfreq_org_depth_max250_allcall%2Ceqtl_Type10_1E-5_MIN_all_10%2Ceqtl_Type12_1E-5_MIN_all_12 (2016 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4931044/)

Non-model organisms

Animals

BovineGenome - http://bovinegenome.org (instance http://www.bovinegenome.org/apollo-lsaa/20/jbrowse/index.html)
OpossumBase http://www.opossumbase.org/
Chinese Hamster - http://www.chogenome.org/JBrowse.php
Animal Genome DB - http://i.animalgenome.org/jbrowse/
Naked mole rat http://naked-mole-rat.org/ (instance http://naked-mole-rat.org/jbrowse/index.html?tracks=region,gene,mRNA&loc=NW_004624913.1:2045721..2060006)
Parus major (bird) https://genomes.bioinf.nioo.knaw.nl/node/279579
Gold colored manakin (bird) - Smithsonian genome collection (https://oris.si.edu/smithsonian-genome-collection) (Manacus Vitellinus) https://oris.si.edu/smithsonian-digital-genome-collection/manacus-vitellinus (instance http://genomics.si.edu.s3-website-us-east-1.amazonaws.com/JBrowse-1.11.4/?loc=scaffold1%3A274416..2232959&tracks=DNA%2Cgenes%2CRepeatMasker&highlight=&tracklist=0&overview=1&nav=1)
Chicken embryonic http://geisha.arizona.edu/geisha/search.jsp?entrez_gene=462937
Chicken repeats http://chicken-repeats.inra.fr/index.php?pages/Galgal5%3A-What-s-new
Metazome (multispecies) https://metazome.jgi.doe.gov/pz/portal.html (instances https://metazome.jgi.doe.gov/jbrowse/index.html)
Pig lncRNA http://lnc.rnanet.org/pid/262/
NABIC - Agricultural animals http://nabic.rda.go.kr/gere/genomeResearchMain.do (cow instance http://nabic.rda.go.kr/jbrowse.do?data=cow
RabGTD - Rabbit http://www.picb.ac.cn/RabGTD/# (2018 pub https://academic.oup.com/database/article/doi/10.1093/database/bay075/5053987)
Goat alternative splicing - http://xufeng.ngrok.xiaomiqiu.cn/jbrowser/JBrowse-1.12.3/index.html?data=goat&loc=NC_005044.2%3A1206.1408&tracks=goat_AS_gtf%2CTotal.bed%2CGenes.bed&highlight= (2018 pub https://www.nature.com/articles/s41598-018-33078-7)
Domestic dog + wild relatives http://bigd.big.ac.cn/idog/ (2018 pub https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky1041/5146205)
Macaque - registration required https://mgap.ohsu.edu/ (2019 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6402181/)
ASlive - Alternative splicing in livestock (2020 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6993437/)
iMarmot http://www.marmotdb.org/ (2020 pub https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6697-7)
Cat genome https://cat.annotation.jp/ (2020 preprint https://www.biorxiv.org/content/10.1101/2020.05.19.103788v1)

Fish

Electric Fish https://efishgenomics.integrativebiology.msu.edu
Asian Seabass - http://seabassgb.sanbi.ac.za (instance http://seabassgb.sanbi.ac.za/jbrowse/?data=seabass_jbrowse)
Common carp, rainbow trout http://www.fishbrowser.org/
Salmon, trout http://salmobase.org/
Goldfish http://nemogenome.org/
Sea lamprey https://genomes.stowers.org/organism/Petromyzon/marinus
Nothobranchius furzeri http://nfingb.leibniz-fli.de/
Seabass http://denovo.cnag.cat/genomes/seabass/
Seriola https://www.serioladb.org/downloads

Invertebrates

Marine genomics - http://marinegenomics.oist.jp/
Mnemiopsis (comc jelly) http://research.nhgri.nih.gov/mnemiopsis/
Echinobase (sea urchin) http://www.echinobase.org (instance http://www.echinobase.org/Echinobase/jbrowse/index.html?data=data_sp&loc=Scaffold1%3A859214..1288779&tracks=DNA&highlight=)
Oyster (built into gigadb data access page) http://gigadb.org/dataset/100240 (instance http://penguin.genomics.cn/jbrowse/index.html?data=100240&loc=PIN_chr1%3A41831034..62750633&tracks=DNA%2CPinctada&highlight=)
PlanMine http://planmine.mpi-cbg.de/planmine/begin.do (2018 pub https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky1070/5212006)
Algae http://mmo.sb-roscoff.fr/jbrowse/
Tardigrade http://kumamushi.org/jbrowse/?data=947166&loc=BDGG01000001.1%3A1..800&tracks=DNA%2Ccds%2Ctrna%2Crrna&highlight=
Planarian dugesia japonica http://www.planarian.jp/ (2018 pub https://link.springer.com/article/10.1186/s40851-018-0102-2)
Bombyx mori (silkworm) http://silkbase.ab.a.u-tokyo.ac.jp/cgi-bin/index.cgi
SCNBase (soybean nematode) https://scnbase.org/ (2019 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853641/)

Insects

AphidBase - http://bipaa.genouest.org/is/aphidbase/acyrthosiphon_pisum/ (http://bipaa.genouest.org/jbrowse_aphid/)
VectorBase (mosquito) https://www.vectorbase.org/
ASGDB (Anopheles sinensis, mosquito) http://www.asgdb.org/
Agambrowser (Anopheles gambiae, mosquito) http://omics.fiu.edu/Agambrowser.html
i5k Workspace@NAL https://i5k.nal.usda.gov/ (instances https://i5k.nal.usda.gov/available-genome-browsers)
BeetleBase - http://beetlebase.org/JBrowse-1.10.5/index.html?data=tcas_4.0
Wintermoth http://www.bioinformatics.nl/wintermoth/jbrowse/?loc=OBRU01_Sc00001%3A196170..294258&tracks=DNA&highlight=
White fly http://whiteflygenomics.org
PTspider Base http://www.e-celldev.jp/pt_spiderbase/ (instance http://www.brh2.jp/jbrowse/Ptep1.0/?loc=Scaffold00547%3A237581..301143&tracks=DNA%2Caug3_gmodels%2Cncbi-AR100&highlight=)
Folsomia+Orchesella http://collembolomics.nl/collembolomics/index.php (instance folsomia http://collembolomics.nl/collembolomics/folsomia/jbrowse/index.html?loc=Fcan01_Sc001%3A11413284..17120148&tracks=DNA&highlight=)
Firefly http://www.fireflybase.org/ (instance http://www.fireflybase.org/jbrowse/) (paper https://www.biorxiv.org/content/early/2017/12/21/237586)
WaspBase http://www.insect-genome.com/waspbase/ (2018 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6146128/)
Hymenoptera - http://hymenopteragenome.org

Plants

Arabadopsis

Araport - https://www.araport.org/ (instance https://apps.araport.org/jbrowse/?data=arabidopsis)
Arabadopsis http://asrp.danforthcenter.org/athaliana
A. thaliana small RNA https://www.molgen.hu-berlin.de/projects-jbrowse-athaliana.html
sORF A. thaliana https://www.biw.kuleuven.be/CSB/ARA-PEPs/
Epigenome https://jbrowse.latrobe.edu.au/germination_epigenome (2017 pub https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1302-3)
ENPG (encyclopedia of plant genome) plantseq.org http://www.plantseq.org/
Stress http://bioinfo.sibs.ac.cn/JBrowse/?data=data_tair10/PcG_vs_stress_v2 (2018 pub https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.14125)

Rice

Rice https://ricebase.org (instance https://ricebase.org/jbrowse_ricebase/current/?data=data&loc=Chr1%3A17307555..25961739&tracks=&highlight=)
Rice SNP-seek http://snp-seek.irri.org/_jbrowse.zul;jsessionid=E05C5B42EB5BE438C189E7CF13B9ACB3?tracks=DNA,msu7gff,msu7snpsv2,msu7indelsv2
IC4R rice http://ic4r.org/ (instance http://visual.ic4r.org/view/?loc=1:2984..10815&tracklist=1&overview=0)
Kitbase http://kitbase.ucdavis.edu/link.html
RicyerDB http://server.malab.cn/Ricyer/
RAP-DB https://rapdb.dna.affrc.go.jp/
Rice stress resistance DB http://bioinformatics.fafu.edu.cn/RSRS/ (2019 pub https://link.springer.com/article/10.1186/s12284-019-0356-0)
Rice Relatives http://ibi.zju.edu.cn/ricerelativesgd/about.php
ROOTOmics https://rootomics.dna.affrc.go.jp/en/research/IR64
RPAN Rice Pangenome Browser http://cgm.sjtu.edu.cn/3kricedb/visualization/?tracks=DNA%2Cgene%2CPF&loc=chr01%3A13229501..13876500&highlight= (2017 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5314802/)

Trees

TreeGenesDB https://treegenesdb.org/Drupal/jbrowse
Hardwood genomics https://www.hardwoodgenomics.org/content/jbrowse
TodoFirGene http://plantomics.mind.meiji.ac.jp/todomatsu/
Rubber tree http://matsui-lab.riken.jp/rubber/ (2018 pub https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4333-y)
Forestry lab http://www.forestrylab.org/bioinfor/db/ASmiR/Jbrowse.php
ForestGEN http://forestgen.ffpri.affrc.go.jp/jp/help.html
Oak genome http://www.oakgenome.fr/?page_id=585 (2018 publication https://www.nature.com/articles/s41477-018-0172-3)
SPTEdb (poplar, etc) http://genedenovoweb.ticp.net:81/SPTEdb/index.php (2018 pub https://academic.oup.com/database/article/doi/10.1093/database/bay024/4925802)
Eucgenie - https://eucgenie.org/ (2019 pub https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.15897)

Wheat

GrainGenes https://wheat.pw.usda.gov/GG3/JBrowse
Triticeae toolbox https://triticeaetoolbox.org
Wheat TILLING database http://www.wheat-tilling.com
Aegilops wheat http://aegilops.wheat.ucdavis.edu/jbrowse/index.html?data=Aet/data (2019 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404623/)
IWGSC (currently password protected) https://urgi.versailles.inra.fr/jbrowseiwgsc/gmod_jbrowse/?data=myData/IWGSC_RefSeq_v1.0
Triticeae Multi-omics Center http://202.194.139.32/
DAWN Diversity Among Wheat geNomes http://crobiad.agwine.adelaide.edu.au/dawn/ (2018 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6296097/)

Legumes

Lentil http://knowpulse.usask.ca/portal/lentil-genome (instance http://knowpulse.usask.ca/portal/jbrowse/Lentil)
PeanutBase https://peanutbase.org/
MedicagoGenome http://www.medicagogenome.org/ (instance http://www.medicagogenome.org/tools/jbrowse)
LegumeInfo https://legumeinfo.org/genomes/
Cool Season Food Legume https://www.coolseasonfoodlegume.org/
Chickpea SNP InDel http://cegresources.icrisat.org/cicarvardb/
Soybean STTM hub https://blossom.ffr.mtu.edu/designindex2.php (2017 MS thesis https://digitalcommons.mtu.edu/cgi/viewcontent.cgi?article=1553&context=etdr)
WildSoyDB http://www.wildsoydb.org/Gsoja_W05/ (2019 pub https://www.ncbi.nlm.nih.gov/pubmed/30872580)
MedicagoHapmap2 http://www.medicagohapmap2.org/

Fruit

CitrusGreening https://citrusgreening.org/jbrowse_citrusgreening/current/
Citrus + pathogens https://www.citrusgenomedb.org/jbrowses
Vaccinium (blueberry) - https://www.vaccinium.org/jbrowses
GDR Genome Database for Rosaceae (strawberry, rose, peach, apple, grape) https://www.rosaceae.org/ (instances https://www.rosaceae.org/tools/jbrowse
Rosaceae transposons RPTEdb http://genedenovoweb.ticp.net:81/RPTEdb/ (2018 pub https://link.springer.com/article/10.1007/s00438-018-1449-y)
Cucumber, melon http://cucurbitgenomics.org/ (instance http://cucurbitgenomics.org/JBrowse/?data=icugi_data/json/cucumber_v2&tracks=DNA,genes)
Melon http://www.melonomics.net/ (2020 pub https://www.frontiersin.org/articles/10.3389/fpls.2019.01815/full)
Peach-VarDB http://hpc-bioinformatics.cineca.it/peach/main
Banana http://banana-genome-hub.southgreen.fr/jbrowse_ma2
Grape - https://urgi.versailles.inra.fr/jbrowse/gmod_jbrowse/?data=myData/Vitis/data_gff
Grape - https://www6.bordeaux-aquitaine.inrae.fr/egfv/Toutes-les-actualites/Genome-browser-RGM
Wine grape & related - http://cantulab.github.io/data.html (2019 pub https://www.g3journal.org/content/9/5/1331)
Apple genome/epigenome https://iris.angers.inra.fr/gddh13/
DBcherry http://cherry.kazusa.or.jp/
Kiwi http://kiwifruitgenome.org/ (2020 pub https://www.nature.com/articles/s41438-020-0338-9)

Tomato+related

Solanaceae (tomato, pepper, tobacco) https://solgenomics.net/
TomatoGenome http://www.tomatogenome.net/
DeenaBio http://jbrowse.deenabio.com/?data=data%2FSolanum_lycopersicum_V2.50%2F&loc=SL2.50ch01%3A1680396..1680447&tracks=ITAG2.4_gene_models%2CDNA%2C360_genomes_SNPs%2Cspecific%2Cnon-specific%2Csuperfamily%2Cmulti-domains%2Cconserved_sites&highlight=
Tomatomics http://bioinf.mind.meiji.ac.jp/tomatomics/

Potato

SpudDB http://solanaceae.plantbiology.msu.edu/

Cotton

CottenGen http://www.cottongen.org/
CottonFGD https://cottonfgd.org (instance https://cottonfgd.org/jbrowse/?data=data%2FGhir-NAU&loc=A01%3A42794028..43538019&tracks=DNA%2CGC%20Content%2Cgene&highlight=)

Multiple species

PlantMethylome and PlantEpigenome- http://epigenome.genetics.uga.edu/PlantMethylome/ and http://epigenome.genetics.uga.edu/PlantEpigenome/index.html
Phytozome - https://phytozome.jgi.doe.gov/ (instances https://phytozome.jgi.doe.gov/jbrowse/index.html)
Plant Small RNA genes http://plantsmallrnagenes.science.psu.edu/
PlantGenIE http://plantgenie.org/ (instance http://popgenie.org/jbrowse
Plant DHS (dnase hypersensitive sites) http://plantdhs.org/
PlaBi (potato, A. thaliana, sugarbeet, brassica napus) http://www.plabipd.de/
PlantCircNet circular RNAs http://bis.zju.edu.cn/plantcircnet/index.php
Lipm https://lipm-browsers.toulouse.inra.fr/
Beans http://beans.cars.desu.edu/
Angiosperms http://www.angiosperms.org/
PlantAPA - http://bmi.xmu.edu.cn/plantapa/help.php (2016 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4914594/)
PlaNC-TE (non-coding and TE) http://planc-te.cp.utfpr.edu.br/ (2018 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6146122/)
PlantPAN http://plantpan.itps.ncku.edu.tw/
Plant co-expression DB https://www.machado.cnptia.embrapa.br/plantannot (demo https://www.machado.cnptia.embrapa.br/plantannot/feature/?feature_id=18243946)
PepperPan (pepper pan genome browser) http://www.pepperpan.org:8012/jbrowse/?data=data%2Fpan&loc=

Maize

Maize inflorescence http://maizeinflorescence.org/jbrowse/index.html?data=maize&loc=chr5%3A14064161..14082560&tracks=GFF%2Cqtl%2Ctophat_ear_base_bigwig%2Ctophat_ear_mid_bigwig%2Ctophat_ear_tip_bigwig&highlight=
Maize gametophyte http://www.maizegametophyte.org/browsers.html
Maize database aMaizing - https://urgi.versailles.inra.fr/jbrowse/gmod_jbrowse/?data=myData/Amaizing/Private
ProFITS (maize signal transduction) http://bioinfo.cau.edu.cn/ProFITS/
MODEM multi-omics http://modem.hzau.edu.cn/
MGR http://maize.plantbiology.msu.edu/ (2019 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6850026/)
MaizeGDB - https://jbrowse.maizegdb.org/

Sweet potato

Sweet potato http://sweetpotato.plantbiology.msu.edu
Ipomoea (sweet potato) https://ipomoea-genome.org/
SweetPotatoBase https://sweetpotatobase.org/search

Other

Brachypodium distachyon http://jbrowse.brachypodium.org
Brassica http://www.bioinformatics.nl/brassica/index.html?data=bras_tp/data
SpirodelaBase http://sviridis.org/jbrowse
Coffee - http://coffee-genome.org/jbrowse
Cassava https://www.cassavagenome.org/?q=page/jbrowse-public
Cucumber alternative splicing CuAS http://cmb.bnu.edu.cn/alt_iso/index.php
Cocoa http://cocoa-genome-hub.southgreen.fr/genome-browser
Amborella http://amborella.huck.psu.edu/fish
MarpolBase http://marchantia.info/
LotusBase https://lotus.au.dk/ (instance https://lotus.au.dk/genome/)
ReefGenomics http://reefgenomics.org/ (example instance http://spis.reefgenomics.org/jbrowse)
Mulberry MnTEdb1 http://genedenovoweb.ticp.net:81/MnTEdb1/
Alfalfa https://www.alfalfatoolbox.org/
Sunflower https://sunflowergenome.org
Barley epigenome https://ics.hutton.ac.uk/barley-epigenome/
Asparagus http://asparagus.uga.edu (2018 pub https://www.nature.com/articles/s41467-017-01064-8)
Pennycress http://pennycress.umn.edu/
Mint (menthe) http://langelabtools.wsu.edu/mgr/genome_browser
Date palm https://jbrowsephoenix.abudhabi.nyu.edu/Jbrowse/JBrowse-1.11.5/?data=dp
NABIC - Agricultural plants http://nabic.rda.go.kr/gere/genomeResearchMain.do (soybean http://nabic.rda.go.kr/jbrowse.do?data=soybean)
Angiosperm conservation http://angiosperm.org/jsp/ping.html (pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798027/)
GnpIS https://urgi.versailles.inra.fr/Tools/GnpIS
Lupin http://www.lupinexpress.org/
Ginsing http://ginsengdb.snu.ac.kr/ (2017 pub https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-018-1282-9)
Olive http://denovo.cnag.cat/genomes/olive/browser_oe6/
Chara https://chara.asrc.kanazawa-u.ac.jp/Cbr1/jbrowse/ (publication https://www.sciencedirect.com/science/article/pii/S0092867418308018)
Medicinal plant genomics http://medicinalplantgenomics.msu.edu/
Tibetan hulless barley http://show.genebang.com/project/gene-browse?n=barley (2018 pub https://www.biorxiv.org/content/early/2018/09/19/409136)
Pineapple http://pineapple.angiosperms.org/pineapple/html/index.html (2017 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6139296/)
Maca http://maca.eplant.org/ (2018 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6195103/)
Adzuki bean+Mung bean http://plantgenomics.snu.ac.kr/mediawiki-1.21.3/index.php/Main_Page
Tea http://tpia.teaplant.org/
SpinachBase http://spinachbase.org/ (2019 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6580994/)
JCDB jatropha curcas http://jcdb.xtbg.ac.cn/ (2019 pub https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6356-z)
Mandarin https://mikan.dna.affrc.go.jp/ (2020 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7272249/)
Lolium https://ics.hutton.ac.uk/jbrowse/lolium/

Microbes/fungus

Virus

Bacteria

Human Oral Microbiome http://www.homd.org/ (instance http://www.homd.org/jbrowse/index.html?data=homd/json/Actinobaculum_oral_taxon_183_F0552_uid173932&tracks=DNA,ncbi_gene,homd_gene)
PATRIC https://patricbrc.org/view/Genome/83332.12#view_tab=browser
PhyTB http://pathogenseq.lshtm.ac.uk/phytblive/index.php
Mycobrowser https://mycobrowser.epfl.ch/genes/MMAR_1971
Pseudomonas http://www.pseudomonas.com/strain/browser
Salmonella http://bioinf.gen.tcd.ie/cgi-bin/salcom.pl?_HL (instance http://bioinf.gen.tcd.ie/jbrowse/?data=salcom&loc=ST4-74.fa%3A1..975873&tracks=DNA%2CCDS%2CsRNA&highlight=)
Salmonella http://opendata.ifr.ac.uk/salseq/
Lyme disease https://lymedisease.med.ucf.edu/
Gluconobacter http://www.gluconobacterfactory.de/
Actinobacter http://bioinf.gen.tcd.ie/acinetocom/
Streptococcus https://veeninglab.com/pneumobrowse (2018 pub http://dx.doi.org/10.1093/nar/gky725)
LeptoDB https://www.leptonet.org.in/ (2018 pub https://academic.oup.com/database/article/doi/10.1093/database/bay057/5037030)
Database of prokaryotic operons http://csbl.bmb.uga.edu/DOOR
EnteroBase - multiple species - https://enterobase.warwick.ac.uk/ (2019 pub https://www.biorxiv.org/content/10.1101/613554v1)
Salmonella NusG-Rho study http://salmonella.cnrs-orleans.fr/NusG-Rho/
Staphylococcus http://rnamaps.unavarra.es/ (2020 pub https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa047/5722047)

Fungus

Neurospoira crassa (fungus) https://neutra.bzh.uni-heidelberg.de/
Agrocybe aegerita mushroom http://www.thines-lab.senckenberg.de/agrocybe_genome
Pichia yeast http://pichiagenome-ext.boku.ac.at:8080/apex/f?p=100:1
Huangjiu Yeast http://www.ligene.cn/hygd/
Yeast strain CEN.PK113-7D http://genomebrowser.uams.edu/cenpk1137/

Parasite

T parva http://igs-ilri.igs.umaryland.edu/eukaryotic.php
B microti http://jbrowse.igs.umaryland.edu/b_microti/
GeneDB (plasmodium, trypaosoma) http://www.genedb.org/Page/jbrowse
LeishDB http://www.leishdb.com/ (instance http://www.leishdb.com/browser)
PamulDB parasite of animals https://biodb.swu.edu.cn/pamuldb/ (2019 pub https://academic.oup.com/database/article/doi/10.1093/database/baz025/5363829)
Trypanosoma brucei http://hank.bio.ed.ac.uk/gRNA/JBrowse-1.16.3/?data=public_data&loc=Tba6ed_v1%3A328..491&tracks=&highlight= (2019 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6868439/)

Other

CyanoBase http://genome.microbedb.jp/CyanoBase
Algae https://greenhouse.lanl.gov/greenhouse/jb/
realDB red algae http://realdb.algaegenome.org/ (2018 pub https://academic.oup.com/database/article/doi/10.1093/database/bay072/5055577)
Burkholderia http://www.burkholderia.com/news
Marine microbes - Marine model organism DB http://mmo.embrc-france.fr/en/exploration/jbrowse
Target-Pathogen DB http://target.sbg.qb.fcen.uba.ar/patho/genome/
Rotifer http://tigriopus.synology.me/
Tetrahymena http://www.jcvi.org/jbrowse/?data=tta2mic
Porcine whipworm http://gasser-research.vet.unimelb.edu.au/ (http://gasser-research.vet.unimelb.edu.au/jbrowse/JBrowse-1.11.2/index.html?data=TsuisMale http://gasser-research.vet.unimelb.edu.au/jbrowse/JBrowse-1.11.2/index.html?data=TsuisFemale)
Tuberculosis vaccine http://crdd.osdd.net/raghava/mtbveb/strain.php?strain=M_avium_K-10
RPFdb riboseq http://sysbio.gzzoc.com/rpfdb/ (2019 pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324049/)
Rotifers http://rotifer.skku.edu:8080/ (2019 pub https://www.researchgate.net/profile/Jae_Seong_Lee2/publication/331423467_The_genome_of_the_marine_monogonont_rotifer_Brachionus_plicatilis_Genome-wide_expression_profiles_of_28_cytochrome_P450_genes_in_response_to_chlorpyrifos_and_2-ethyl-phenanthrene/links/5cf4d7d4a6fdcc84750028ab/The-genome-of-the-marine-monogonont-rotifer-Brachionus-plicatilis-Genome-wide-expression-profiles-of-28-cytochrome-P450-genes-in-response-to-chlorpyrifos-and-2-ethyl-phenanthrene.pdf)
ParameciumDB https://paramecium.i2bc.paris-saclay.fr/ (2019 pub https://www.ncbi.nlm.nih.gov/pubmed/?term=31733062)
Cyanobacteria http://application.sb-roscoff.fr/cyanorak/

Workflows/platforms/concepts

Millstone https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5445467/
myGenomeBrowser https://bbric-pipelines.toulouse.inra.fr/myGenomeBrowser
IVAG https://genominfo.org/m/journal/view.php?doi=10.5808/GI.2017.15.4.178 (features gwasviewer)
CoGe https://genomevolution.org/
WikiGenomes https://wikigenomes.org
FISH oracle http://fishoracle.zbh.uni-hamburg.de:8080/fishoracle/ (expired https)
WebApollo genome annotation http://genomearchitect.github.io/
GenSAS genome annotation pipeline https://www.gensas.org/
PhyloNode http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0175480
proBAM protein encoded BAM in jbrowse http://proteogenomics.zhang-lab.org/ (pub https://www.biorxiv.org/content/biorxiv/early/2017/06/20/152579.full.pdf)
EDGE bioinformatics platform https://github.com/LANL-Bioinformatics/EDGE
FALDO https://www.biorxiv.org/content/early/2014/02/02/002121
iPlant JBrowse MAKER integration https://pods.iplantcollaborative.org/wiki/display/Events/Exploring+MAKER-P+output+with+JBrowse+in+Atmosphere
Galaxy JBrowse wrapper readme https://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=a3e608531354bfa6&render_repository_actions_for=galaxy&tool_config=%2Fsrv%2Ftoolshed%2Fmain%2Fvar%2Fdata%2Frepos%2F001%2Frepo_1536%2Fjbrowse.xml&changeset_revision=7342f467507b
Galaxy+Apollo+JBrowse http://gxaa.readthedocs.io/en/latest/doc/Apollo.html
Afra genome annotation http://afra.sbcs.qmul.ac.uk/
Snippy workflow http://sepsis-omics.github.io/tutorials/modules/snippy/
Prokka workflow https://slugger70.github.io/tutorials/modules/prokka/
CyVerse DNA Subway redline genome annotation https://learning.cyverse.org/projects/dnasubway_guide/en/latest/step3.html
BioNanoAnalyst https://github.com/AppliedBioinformatics/BioNanoAnalyst (pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493081/)
JBrowse ADAM https://github.com/FusionWorks/jbrowse-adam
Vagrant JBrowse https://github.com/Smithsonian/vagrant-jbrowse
KBase JBrowse https://github.com/kbaseapps/kb_GenomeBrowser
JBrowse assembler SPAdes->JBrowse https://github.com/kadhirvelm/jbrowse_assembler
JBrowse tools https://github.com/bellerbrock/jbrowse_tools
G-OnRamp - http://gonramp.org https://ir.library.illinoisstate.edu/cgi/viewcontent.cgi?article=1162&context=beer
MuGVRE (multiscale genomics 3D/4D) https://www.multiscalegenomics.eu/ (2019 pub https://www.biorxiv.org/content/biorxiv/early/2019/04/09/602474.full.pdf)

CRISPR

CRISPR-PLANT https://www.genome.arizona.edu/crispr/jbrowse/
Fly RNAi www.flyrnai.org
CRISPR-RT http://bioinfolab.miamioh.edu/CRISPR-RT/interface/Installation.php CRISPR-DT bioinfolab.miamioh.edu/CRISPR-DT CT-FINDER bioinfolab.miamioh.edu/ct-finder/
Cas-Database http://www.rgenome.net/cas-database/
grID crispr.technology http://crispr.technology/browser/?loc=chr1%3A99685667..149535791&tracks=DNA&highlight=
piRNAquery http://bicresources.jcbose.ac.in/zhumur/pirnaquest/JBrowse-1.9.8/index.php?data=sample_data/json/human/data&loc=chr1:1..20000000&tracks=DNA,,,,,,,,,,,,

Other

CaZY http://www.cazy.org/PULDB/jbrowse.php?data=species%2F130&loc=Ga0105823_103%3A76907..86749&tracks=Protein-coding%20genes%2CPredicted%20PULs%2CCAZyme%20clusters&highlight=
MethSMRT - cross species browsers http://sysbio.gzzoc.com/methsmrt/
REDIPortal - A-to-I editing database http://srv00.recas.ba.infn.it/atlas/ (instance http://srv00.recas.ba.infn.it/atlas/jbrowse.html)
Lnc2Meth http://bio-bigdata.hrbmu.edu.cn/Lnc2Meth/browse.jsp
CLIP-SEQ browser http://lulab.life.tsinghua.edu.cn/clipdb/
ChIP-Base http://rna.sysu.edu.cn/chipbase/
tRF-finder http://rna.sysu.edu.cn/tRFfinder/browser.php?loc=tRNA-Gln-TTG-3-3:1..101
PopFly - http://popfly.uab.cat/
AURA - Atlas of UTR regulatory activity http://aura.science.unitn.it/search_gene/?activeTab=0&organism=hg19&genename=MYC
CAPSID - https://github.com/capsid/capsid/wiki/Tutorial
Togogenome http://togogenome.org/gene/9913:BRB
RPFDB ribosome protected mRNA fragments ]multi species] http://sysbio.sysu.edu.cn/rpfdb (instance http://sysbio.gzzoc.com/rpfdb/jbrowse/index.html?data=rpf_data%2Fhuman&loc=rcan1&tracks=Human_ref_seq%2CDNA%2CGSE22004_SRX021966_coverage)
OpenLooper https://openlooper.hgc.jp/JBrowse/index.php
ChIP-Array 2 http://jjwanglab.org/chip-array/about (2015 pub https://www.ncbi.nlm.nih.gov/pubmed/25916854)
SPAR - small RNA https://spar.lisanwanglab.org/ (2018 pub https://academic.oup.com/nar/article/46/W1/W36/4992647)

Plugins

New track types

MultiBigWig https://github.com/cmdcolin/multibigwig
MultiVariantViewer https://github.com/elsiklab/multivariantviewer
SashimiPlot https://github.com/cmdcolin/sashimiplot
GCContent https://github.com/cmdcolin/gccontent
GCCoverage https://github.com/cmdcolin/gccontent
GWASViewer https://github.com/cmdcolin/gwasviewer
MAFViewer https://github.com/cmdcolin/mafviewer
BioNano https://github.com/bionanogenomics/JBrowsePlugin
Methylation https://github.com/bhofmei/jbplugin-methylation
StandedPlot https://github.com/bhofmei/jbplugin-strandedplot
ProportionalMultiBw https://github.com/cancerit/proportionalmultibw
BLAT/BLAST views https://github.com/goeckslab/JBrowse_plugins/tree/master/js
PydginElastic XYPlot https://github.com/tottlefields/jbrowse-pydginelastic
JBrowse SNPViewer https://github.com/martinSergeant/jbrowse_snp_viewer
FrameViewer https://github.com/cmdcolin/frameviewer
ColorByCDS https://github.com/cmdcolin/colorbycds
NucDens https://github.com/bhofmei/jbplugin-nucdens
VariantEffect https://github.com/hans-vg/jbplugin-varianteffect

Backend adapters

MyVariantViewer https://github.com/cmdcolin/myvariantviewer
GA4GHViewer https://github.com/cmdcolin/ga4ghviewer
EnsemblVariants https://github.com/Arabidopsis-Information-Portal/EnsemblVariants
ElasticSearch https://github.com/cmdcolin/jbrowse_elasticsearch
1001 Genomes (araport) https://github.com/Arabidopsis-Information-Portal/1001GenomesVariants
CyVerse https://github.com/Arabidopsis-Information-Portal/CyverseRemoteTracks
Araport https://github.com/Arabidopsis-Information-Portal/AraportJBPlugin

UI modifiers

HierarchicalCheckbox https://github.com/bhofmei/jbplugin-hierarchicalcheckbox
TrackScores https://github.com/bhofmei/jbplugin-trackscores
SmallRNA https://github.com/bhofmei/jbplugin-smallrna
Araport ComboTrackSelector https://github.com/Arabidopsis-Information-Portal/jbrowse/tree/stable/plugins/ComboTrackSelector
SwitchTrackSelector http://staging.wormbase.org/tools/genome/jbrowse-simple/plugins/SwitchTrackSelector/js/main.js
AliasRefSeqs https://github.com/rbuels/aliasrefseqs-jbrowse-plugin

Tools

Screenshot https://github.com/bhofmei/jbplugin-screenshot
Fullscreen https://github.com/awilkey/fullscreen-jbrowse
Araport SeqLighter https://github.com/Arabidopsis-Information-Portal/SeqLighter
FeatureSequence https://github.com/tsaari88/FeatureSequence
RestrictionSearch https://github.com/scottcain/RestrictionSearch
MotifSearch https://github.com/scottcain/MotifSearch
MotifFinder https://github.com/scottcain/MotifFinder
PrimerDesign https://github.com/jimhu-tamu/hulab-jbrowse
WebApollo https://github.com/GMOD/Apollo
Genovo https://github.com/igemsoftware/Shenzhen_BGIC_0101_2013/tree/master/plugins/Genovo (https://github.com/gongjianhui-bgi/Genovo)
ManyTracks https://github.com/cmdcolin/manytracks

Wrapper systems

CoGE https://github.com/LyonsLab/coge/tree/master/web/js/jbrowse/plugins/CoGe
Dynamix http://gbcs.embl.de/portal/tiki-index.php?page=JBrowse+Dynamix+Plugin
SeqsLab http://seqslab.net/
Capsid https://github.com/capsid/capsid

Other/experimental

PubAnnotation https://github.com/rbuels/JBrowse_PubAnnotation
LinkedReadsViewer (experimental) https://github.com/cmdcolin/linkedreadsviewer
Remote BLAST https://github.com/cmdcolin/remoteblast
EncodePlugin https://github.com/cmdcolin/encodeplugin

Old JBrowse instances

For historical perspective these are fun to view

Genomes Unzipped http://genomesunzipped.org/jbrowse/

Dead links

Pangolin genome database
MabsBase http://mabscessus.um.edu.my/
Staphylococcus http://staphylococcus.um.edu.my/index.php/home/main
Cnidarian http://cnidarians.bu.edu/EdwardBase/cgi-bin/index.cgi
Helicobacter http://helicobacter.um.edu.my/index.php/home/main
Vibrio http://vibrio.um.edu.my/index.php/home/main
DNA methylome http://www.dnamethylome.org/
Pineapple http://peach.fafu.edu.cn/html/jbrowse/JBrowse-1.11.5/?data=Pineapple_genome_project (available at phytozome)
RMbase http://mirlab.sysu.edu.cn/rmbase/
NCBI Hackathon Staph viewer https://github.com/NCBI-Hackathons/Staph_aureus_viewer
RPFdb http://sysbio.gzzoc.com/rpfdb/
GAN Nicotiana http://biodb.sdau.edu.cn/gan/ (2018 pub https://academic.oup.com/database/article/doi/10.1093/database/bay001/4898179)
RegulonDB E.coli K12 - http://regulondb.ccg.unam.mx/central_panel_menu/integrated_views_and_tools_menu.jsp claims to use jbrowse in v10.5 but not clear where it is
Wheat http://tcap.pw.usda.gov/jbrowse
Sugarbeet https://jbrowse.cebitec.uni-bielefeld.de/RefBeet1.5/

Credits

Some sources gathered from http://gmod.org/wiki/GMOD_Users

Notes

Some older instances may not load on TouchScreen due to a bug that was fixed in more recent versions of JBrowse. The javascript console will give a fatal error loading dgrid/TouchScroll. No workaround is available AFAIK

Feel free to provide feedback and better species categorizations :)

Read the original on github.com ↗