unique379r/awesome-genome-visualization

A list of interesting genome browser or genome-browser-like implementations

awesome-genome-visualization

A list of interesting genome visualizers, genome browsers, or genome-browser-like implementations

See the new companion website here https://cmdcolin.github.io/awesome-genome-visualization/

Follow the Twitter account here too :) https://twitter.com/awesomegenomev1

Note that the organization here is a best effort categorization for general tags applied to these tools

General

• Genoverse (img)
• BasePlayer (pub) (img)
• Celera genome browser (img)
• IGB (pub) (img)
• IGV (img)
• Savant (pub) (img)
• Tablet (img)
• Biodalliance (img)
• Ensembl genome browser (img)
• Ensembl genome browser 2020 edition (img)
• GBrowse+GBrowse 2 (img)
• GenomeMaps (pub)
• Gosling (img)
• HiGlass (img)
• IGV.js (img)
• JBrowse (See also JBrowse plugin registry https://gmod.github.io/jbrowse-registry. Runs on the web or as a desktop app using Electron) (img)
• JBrowse 2 (See gallery for more examples https://jbrowse.org/jb2/gallery) (img)
• Kero-BROWSE (img)
• NCBI Genome Data Viewer (img)
• Nucleome browser (img)
• Pileup.js (img)
• Trackster (img)
• UCSC genome browser (img)
• Valis browser (img)
• WashU epigenomics browser (img)
• Zenbu (img)

Commercial

• 10x genomics/Loupe (img)
• Alamut (img)
• ATCC Genome Portal (American Type Culture Collection) (img)
• Benchling (img)
• CLC Genomics workbench (img)
• DNASTAR (img)
• Geneious (img)
• Genestack (img)
• Golden Helix (img)
• Lucid viewer (img)
• MacVector (img)
• Persephone (img)
• SnapGene (img)
• Strand NGS (img)
• Bionano (img)
• Circa (img)

MSA

• AA (also see STRAP) (img)
• abrowse (img)
• alignment.js (img)
• AlignmentComparator (Uses http://bioinfweb.info/LibrAlign/) (img)
• AlignmentViewer (img)
• AliView (img)
• BioJS/MSA (pub) (img)
• Boxshade (img)
• ESPript (img)
• Jalview (img)
• JSAV (pub) (img)
• LogoJS (img)
• MSABrowser (img)
• msaR (uses BioJS/MSA) (img)
• MView (img)
• NCBI MSA Viewer (img)
• pyBoxshade (also see boxshade)
• pymsaplotter (img)
• React MSAViewer (img)
• react-msaview (img)
• seqotron (img)
• STRAP (also see AA) (img)
• TeXShade (img)
• Wasabi (img)
• SNPViz (img)
• ALVIS (MSA viewer) (Introduces sequence bundles concept, also see web app version https://www.ebi.ac.uk/goldman-srv/sequencebundles/) (pub) (img)
• alignfigR (img)

CNV

• aCNVViewer (pub) (img)
• CNVkit (pub) (img)
• BAMScale (pub) (img)
• cnvCurator (pub) (img)
• GenomeSpy (img)
• GenomePaint (See also gallery here https://genomepaint.stjude.cloud/#figures) (pub) (img)
• covviz (img)
• PURPLE (intermutation-distance rainfall plots/katagesis plots are not technically in genomic coordinates, but do indicate genomic cluster of variatnts) (img)
• bctools cnv (img)
• mocha (Has a full analysis pipeline associated with end result visualizations) (img)
• genevisR (img)
• copynumber (img)

Static

• BAMSnap (img)
• ChIA-Pipe (pub) (img)
• CNView (img)
• CNVPlot (img)
• CNVpytor (img)
• DNAPlotLib (img)
• ExonIntron (img)
• FeatureViewer (img)
• Geneviz (img)
• Genome STRiP (img)
• GenomeTools (img)
• GenomeView (img)
• genoPlotR (img)
• ggbio (pub) (img)
• GGgenes (img)
• GGsashimi (img)
• gtrellis (img)
• Gviz (img)
• Hagfish (img)
• HiCPlotter (img)
• JVarKit/BamToSVG (img)
• Lollipops (img)
• Mason (img)
• Methplotlib (img)
• Pairoscope (img)
• pauvre (pub) (img)
• pyGenomeTracks (img)
• RACER (img)
• RepViz (img)
• Samplot (img)
• SashimiPlot (img)
• shabam (img)
• SparK (pub) (img)
• Spliceclust (img)
• Sushi (img)
• svist4get (pub) (img)
• svv (img)
• svviz (pub) (img)
• svviz2 (pub) (img)
• trackViewer (img)
• circlize (img)
• mummer2circos (img)
• cgplot (img)
• bcftools roh (Plots runs of homozygosity, has interactive plot-roh.py helper too) (img)

Gene fusion

• Chimeraviz (img)
• clinker (gene fusion) (pub) (img)
• arriba (pub) (img)
• FusionInspector (Uses igv.js) (img)

Alignment viewer

• GenomeView (java app) (img)
• pyBamView
• Chromatic (pub) (img)
• Gambit (img)
• LookSeq (img)
• udon (Uses an advanced data structure for pileup, so visually a basic example but likely just a small demo) (img)

Comparative

• GSSPlayground (img)
• Aequatus (img)
• AliTV (img)
• Artemis comparison tool (ACT) (img)
• Biodalliance comparative demo (img)
• Chromatiblock (pub) (img)
• CMap (img)
• CoGe (img)
• Comparative assembly hub / "snake track" (pub) (img)
• CrossBrowse (pub) (img)
• CVit (img)
• Cvit.js (img)
• EasyFig (pub) (img)
• GBrowse_syn (img)
• Genome Context Viewer (img)
• Genome-plots-processing (img)
• Genomicus (img)
• gggenomes (img)
• GIVE (img)
• mauve-viewer (img)
• MCScan (python version) (img)
• MCScanX (img)
• mGSV (multiple genome synteny viewer)
• MizBee (pub) (img)
• Multiple genome viewer (img)
• OMA local synteny browser (img)
• pafr (img)
• Parasight (Examples at https://ratparalogy.gs.washington.edu/) (img)
• syri/plotsr (img)
• progressiveMauve viewer (img)
• SyMap (pub) (img)
• Synima (pub) (img)
• Synteny browser (img)
• SynTView (pub) (img)
• SynVisio (img)
• Tripal MapViewer (img)
• VISTA browser (img)
• XMatchView (img)
• LinearDisplay.pl (img)
• FastANI (img)
• clinker (pub) (img)
• RectChr (img)

Single cell

• Millefy (img)
• gingko (img)
• copykat (img)
• scCNV_heatmap (img)
• casper (pub) (img)

GWAS

• PureScript genetics browser (img)
• Locuszoom (Also see locuszoom.js http://locuszoom.org/locuszoomjs.php) (img)
• LDBlockShow (pub) (img)

Dotplot

• shinyChromosome (pub) (img)
• D-GENIES (img)
• Delly-maze (img)
• Discoplot (img)
• Dot (img)
• Dotlet (img)
• Dotplot (chirimoyo)
• iLambda/Dotplot
• dotPlotly (img)
• Dottup (also seen here http://eichlerlab.gs.washington.edu/publications/chm1-structural-variation/data/GRCh37/heterochromatic_extensions.pdf) (img)
• FlexiDot (img)
• Gepard (pub) (img)
• Jdot (img)
• last-dotplot (img)
• mcutils (https://twitter.com/mjpchaisson/status/1040363992206569472) (img)
• Minidot (img)
• Mummer-idotplot
• Mummerplot (img)
• ggplot2 mummerplot (img)
• Redottable (img)
• syntenyPlotByR (img)
• Dotter (pub) (img)
• JGI/IMG (Dotplot use MUMmer) (img)
• MashMap (img)

Gene structure

• TnT (img)
• Apollo aka WebApollo (img)

Microbiology

• Edinburgh-Genome-Foundry/DnaFeaturesViewer (pub) (img)

Graph

• AGB assembly graph browser (pub)
• Bandage (pub) (img)
• gfaestus (img)
• gGnomes.js (img)
• graphgenomeviewer (img)
• MoMi-G (img)
• odgi draw + odgi viz (Example from https://github.com/pangenome/pggb) (img)
• sequence tube map (img)
• Shasta (Uses graphviz) (img)
• LINX (part of the PURPLE/GRIDSS/LINX pipeline) (img)
• GfaViz (pub) (img)

Text based

• Alan (img)
• Alv (img)
• ASCIIGenome (img)
• Bamcov (img)
• bioSyntax
• BLAST+ (reading -outfmt 0 pairwise output is the original CLI bioinformatics!)
• Hapviz
• plotReads (img)
• Rna Alignment Viewers (pub) (img)
• Sam2pairwise
• Samtools depth visualization (img)
• Samtools tview (img)
• SvABA (img)
• VizAln (from HipSTR) (img)

Circular

• Anvio
• BioCircos.js (img)
• Circleator (img)
• Circos
• CircosJS (img)
• DNAPlotter (img)
• GenomeProjector (pub) (img)
• JupiterPlot (img)
• OGDRAW (pub) (img)
• Gview (img)

Synthetic biology

• seqviz (img)
• ApE (a plasmid editor) (img)
• Chopchop (img)

Special-purpose

• Apollo (pub) (img)
• D3GB (img)
• DNASkittle (img)
• EaSeq (pub) (img)
• FluentDNA (img)
• Gnomad browser (img)
• Hawkeye (pub) (img)
• IslandPlot (D3, SVG) (img)
• MagicViewer (pub) (img)
• Panoptes (img)
• MapView (links in original paper are dead, but URL provided here works) (pub) (img)
• NGB (img)
• SeqCover (img)
• SEQing (img)
• SFARI (img)
• Short read assembly browser (img)
• SNPitty (pub) (img)
• Staden (img)
• TASUKE (img)
• TE-nest (download link unknown) (img)
• Transposcope (img)
• UGENE (img)
• Varsome (img)
• Vials
• wasm bigwig demo browser (img)

SV

• Ribbon (pub) (img)
• Gremlin (img)
• InGAP-SV (img)
• Introgression browser (pub) (img)
• SplitThreader (img)
• SMRT View (img)
• asgart (pub) (img)

Expression

• GTEX Locus browser (img)

Population

• GWAS catalog browser (img)
• Human genome dating (made with vega/d3) (img)
• PopSV (img)
• SWAV (pub) (img)

Assembly QC

• Icarus (img)

Exotic

• BigTop (img)
• Cylindrical alignment app (img)
• sockeye (pub) (img)
• spinteny (img)

Data grid

• BrowseVCF (pub)
• CuteVCF

Epigenomics

• Chip Monk (Also see SeqMonk https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) (img)
• Chipster (Copy number tutorial https://chipster.csc.fi/manual/cn-tutorial.pdf) (img)
• cisGenome Browser (img)
• Epilogos (img)
• Epiviz (pub) (img)
• HiC browser
• HiPiler (img)
• Juicebox (pub) (img)
• Juicebox.js (pub) (img)
• Peax (img)

Ideogram

• chromoMap (img)
• eweitz/Ideogram (img)
• Ideogram (img)
• Ideoplot
• karyoploteR (img)
• KaryotypeSVG (img)
• NCBI Genome Decoration (img)
• UCSC Genome Graphs (img)

Mobile

• iGenomics (img)

Pangenome

• Pan-Tetris (pub) (img)
• Panacaea (img)
• Panache (img)
• panX (pub) (img)
• RPAN (3kricedb) (img)

Protein

• Protael (pub) (img)
• ProteinPaint (pub) (img)
• pViz (img)

Heatmap

• UCSC Xena (img)
• VIVA (img)

Repeats

• REPAVER (pub) (img)

Historical

• Internet Contig Explorer (pub) (img)

QC

• ALVIS (chimeric alignment viewer) (pub) (img)
• vcfR (image shows chromoqc output) (img)

Methylation

• NanoMethViz (pub) (img)
• AnnoJ (See list of instances of the browser here https://ecker.salk.edu/genome-browser/) (img)

Phylogenetics

• Nextclade (Related usage on nextstrain app also) (img)

Uncategorized

• methylartist (img)

Other lists

• Awesome Bioinformatics
• Genocat large collection of genomic visualizations with great review paper accompaniment https://onlinelibrary.wiley.com/doi/full/10.1111/cgf.13727
• awesome-biological-visualizations

Send in PRs for more stuff!

License

This README.md and TOOLS.json are CC0 https://creativecommons.org/publicdomain/zero/1.0/

Remember

Always remember, "YOU ARE AWESOME"!!! (read in Ben Busby's voice, thanks Ben for reminding us of this always :)