rnaimehaom / 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 on the GitHub README here is a best effort categorization using the first tag applied to each tool, but tools can have multiple tags too. See the website to see all tags applied to tools

Note: This list runs the gammut from bespoke and simple to more general-purpose and complex tools. Some are historical, or may be for more visual inspiration only

I also encourage you to make your own visualization, things like R make this so much easier! But also consider making your visualization code re-usable for the wider community! And feel free to send PRs for more tools!

General

• Genoverse (img)
• BasePlayer (img)
• Celera genome browser (img)
• IGB (img)
• IGV (img)
• Savant (img)
• Tablet (img)
• Biodalliance (img)
• Ensembl genome browser (img)
• Ensembl genome browser 2020 edition (img)
• GBrowse 2 (Original gbrowse paper https://doi.org/10.1101/gr.403602) (img)
• GenomeMaps (img)
• 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 (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) (img)
• NCBI Genome Data Viewer (img)
• Nucleome browser (github at https://github.com/nucleome) (img)
• Pileup.js (img)
• Trackster (img)
• UCSC genome browser (img)
• Valis browser (img)
• WashU epigenomics browser (features redesign, there is also a legacy version) (img)
• Zenbu (img)
• UTGB (University of Tokyo Genome Browser) (img)
• Argo (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)
• ERGO (img)

MSA

• AA (alignment annotator) (also see STRAP) (img)
• abrowse (img)
• alignment.js (img)
• AlignmentComparator (Uses http://bioinfweb.info/LibrAlign/) (img)
• AlignmentViewer (img)
• AliView (img)
• BioJS/MSA (img)
• rMSA (Can automate boxshade) (img)
• Boxshade (Also available as a command line tool with apt install boxshade. See also rMSA which can automate running boxshade from within R) (img)
• ESPript (img)
• Jalview (img)
• JSAV (img)
• MSABrowser (img)
• msaR (uses BioJS/MSA) (img)
• MView (img)
• NCBI MSA Viewer (img)
• pyBoxshade (also see boxshade) (img)
• pymsaplotter (img)
• React MSAViewer (img)
• react-msaview (img)
• seqotron (img)
• STRAP (also see AA) (img)
• TeXShade (img)
• Wasabi (img)
• SNIPViz (img)
• ALVIS (MSA viewer) (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/) (img)
• alignfigR (img)
• alen (img)
• ProViz (See also alphafold visualization as tracks http://slim.icr.ac.uk/projects/alphafold?page=alphafold_proviz_homepage) (img)
• MEGA-X (original paper from 1994 but actively updated. requires EULA for download) (img)
• AliTreeViz (img)
• ete (img)
• ggtree (see https://yulab-smu.top/treedata-book/chapter7.html?q=msa#msaplot for MSA example) (img)
• seqvisr (img)
• Seaview (img)
• CIAlign (Has useful utility functions to clean gaps and trim MSAs) (img)
• ggmsa (See also ggtree) (img)
• CView (img)

Logo

• LogoJS (img)

CNV

• aCNVViewer (img)
• CNVkit (img)
• BAMScale (img)
• cnvCurator (img)
• GenomeSpy (img)
• GenomePaint (Not open source) (img)
• covviz (img)
• PURPLE (intermutation-distance rainfall plots/katagesis plots are not technically in genomic coordinates, but do indicate genomic cluster of variatnts) (img)
• bcftools cnv (img)
• mocha (Has a full analysis pipeline associated with end result visualizations) (img)
• genevisR (img)
• copynumber (img)
• SnoopCGH (img)
• Genovar (img)
• CNANorm (img)
• Orchestral (img)
• CNSpector (img)
• sequenza (also see https://sequenzatools.bitbucket.io/#/home) (img)

Static

• BAMSnap (img)
• ChIA-Pipe (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 (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 (img)
• pyGenomeTracks (img)
• RACER (img)
• RepViz (img)
• Samplot (img)
• SashimiPlot (img)
• shabam (img)
• SparK (img)
• Spliceclust (img)
• Sushi (img)
• svist4get (img)
• svv (img)
• svviz (img)
• svviz2 (img)
• trackViewer (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 software) (img)
• arriba (img)
• FusionInspector (Uses igv.js) (img)
• MAVIS (img)

Alignment viewer

• GenomeView (java app) (img)
• pyBamView (See supplementary info for more figures, supports padded SAM/BAM which is fairly rare) (img)
• Chromatic (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 (img)
• CMap (img)
• CoGe (img)
• Comparative assembly hub / "snake track" (img)
• CrossBrowse (img)
• CVit (img)
• Cvit.js (img)
• EasyFig (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) (img)
• MizBee (img)
• Multiple genome viewer (img)
• OMA local synteny browser (img)
• pafr (img)
• Parasight (Examples at https://ratparalogy.gs.washington.edu/) (img)
• progressiveMauve viewer (img)
• SyMap (img)
• Synima (img)
• Synteny browser (img)
• SynTView (img)
• SynVisio (img)
• Tripal MapViewer (img)
• VISTA browser (img)
• XMatchView (img)
• LinearDisplay.pl (readme says to cite this paper) (img)
• FastANI (img)
• clinker (img)
• RectChr (img)
• pretzel (img)
• PipMaker (See also MultiPipMaker http://pipmaker.bx.psu.edu/pipmaker/mpm-example/index.html) (img)
• WGDI (img)
• BRIG (img)
• GENESPACE (img)
• miropeats (image from 2021 paper https://www.biorxiv.org/content/10.1101/2021.12.08.471837v1.full.pdf) (img)
• syntenyPlotteR (img)
• chromoMap (img)
• SafFire (img)
• SimpleSynteny (img)
• Cinteny (img)
• AutoGraph (img)
• EvolutionHighway (The 'evolutionary highway' image type is reproduced in some other packages e.g. https://github.com/marta-fb/syntenyPlotteR, paper https://doi.org/10.1126/science.1111387) (img)
• Smash++ (img)
• plotsr (Blurs the line between synteny and SV visualization, a good thing!) (img)
• GenomeMatcher (img)
• SynBrowse (img)
• Sybil (Download https://sourceforge.net/projects/sybil/) (img)
• SyntenyPortal (img)
• CHROMEISTER (img)
• r2cat (img)
• SequenceSurveyor (img)
• BactoGENIE (img)
• PSAT (img)
• TreeBrowser (MicrobesOnline) (img)
• Combo (Based on the tool 'Argo') (img)
• GenomicBreaks (img)
• GenomeSyn (img)
• CrowsNest (img)
• GGisy (img)
• multiGenomicContext (img)
• AccuSyn (img)

Single cell

• Millefy (img)
• gingko (img)
• copykat (img)
• scCNV_heatmap (img)
• casper (img)
• ArchR (img)
• numbat (img)

GWAS

• PureScript genetics browser (img)
• Locuszoom (Also see locuszoom.js http://locuszoom.org/locuszoomjs.php) (img)
• LDBlockShow (img)
• ggplot2 manhattan plot (This is not a preconfigured tool but a blog post tutorial with tidy data and ggplot2) (img)
• CMPlot (img)
• GeneticsMakie.jl (img)

Dotplot

• shinyChromosome (img)
• D-GENIES (img)
• Delly-maze (see also https://www.gear-genomics.com/maze/) (img)
• Discoplot (img)
• Dot (Python data preparation script) (img)
• Dotlet (The original publication was 2000 but updated ~2020 with reactjs) (img)
• Dotplot (chirimoyo)
• iLambda/Dotplot
• dotPlotly (img)
• Dottup (also seen here http://eichlerlab.gs.washington.edu/pubs/chm1-structural-variation/data/GRCh37/heterochromatic_extensions.pdf) (img)
• FlexiDot (img)
• Gepard (img)
• Jdot (img)
• last-dotplot (img)
• mcutils (https://twitter.com/mjpchaisson/status/1040363992206569472) (img)
• Minidot (img)
• Mummer-idotplot
• Mummerplot (img)
• ggplot2 mummerplot (img)
• Redotable (img)
• syntenyPlotByR (img)
• Dotter (img)
• JGI/IMG (Dotplot use MUMmer) (img)
• MashMap (img)
• oxford-plots (Has nice description of a synteny pipeline here https://github.com/jherrero/oxford-plots/blob/master/examples/pig_X_Y.txt) (img)
• DAGchainer (img)
• local-rearrangements (Can color dotplots with annotations for e.g. exons, transposons, low complexity regions. See also last-dotplot. Nice figure using it here https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-020-00762-1/figures/4) (img)

Gene structure

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

Microbiology

• Edinburgh-Genome-Foundry/DnaFeaturesViewer (img)
• GeneViTo (img)
• GECO (img)
• GeCoViz (img)

Graph

• AGB assembly graph browser
• Bandage (See also BandageNG https://github.com/asl/BandageNG) (img)
• gfaestus (See demo video displaying GFF3 annotations on graph https://www.youtube.com/watch?v=A-HnKXIrJl4) (img)
• graphgenomeviewer (img)
• MoMi-G (img)
• odgi draw + odgi viz + odgi inject (Example from https://github.com/pangenome/pggb, see also gene arrow map https://odgi.readthedocs.io/en/latest/rst/tutorials/injecting_gene_arrows.html) (img)
• sequence tube map (img)
• Shasta (Uses graphviz) (img)
• LINX (part of the PURPLE/GRIDSS/LINX pipeline) (img)
• GfaViz (img)
• panGraphViewer (img)
• IGGE (Not open source) (img)

SV

• gGnomes (img)
• gGnomes.js (img)
• Ribbon (img)
• Gremlin (img)
• InGAP-SV (img)
• Introgression browser (img)
• SplitThreader (img)
• SMRT View (wiki page https://github.com/PacificBiosciences/DevNet/wiki/SMRT-View) (img)
• asgart (img)
• NeoLoopFinder (img)
• SVPV (img)
• AmpliconArchitect (The term amplicon refers essentially to extrachromosomal DNA in cancer) (img)

Text based

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

Circular

• Anvio
• BioCircos.js (img)
• Circleator (img)
• circlize (img)
• Circos (the github repo is not up to date with the latest code) (img)
• CircosJS (img)
• DNAPlotter (img)
• GenomeProjector (img)
• JupiterPlot (img)
• OGDRAW (img)
• Gview (img)
• RegulomeExplorer (img)
• CGView (See also CGView comparison tool and other related https://paulstothard.github.io/cgview_comparison_tool/) (img)
• pyCircos (See also https://github.com/ponnhide/plasmidviewer) (img)

Synthetic biology

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

Special-purpose

• Apollo (img)
• D3GB (img)
• DNASkittle (img)
• EaSeq (img)
• FluentDNA (img)
• Gnomad browser (img)
• Hawkeye (img)
• IslandViewer and IslandPlot (web app using it here https://pathogenomics.sfu.ca/islandviewer uses D3, SVG) (img)
• MagicViewer (img)
• Panoptes (img)
• MapView (links in original paper are dead, but URL provided here works) (img)
• NGB (img)
• SeqCover (img)
• SEQing (img)
• SFARI (img)
• Short read assembly browser (img)
• SNPitty (img)
• Staden (img)
• TASUKE (info about multi-genome-browser https://tasuke.dna.affrc.go.jp/) (img)
• TE-nest (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/) (img)
• Transposcope (img)
• UGENE (img)
• Varsome (img)
• Vials
• wasm bigwig demo browser (img)

Expression

• GTEX Locus browser (img)

Population

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

Assembly QC

• Icarus QUAST (img)

Exotic

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

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 (img)
• HiPiler (img)
• Juicebox (img)
• Juicebox.js (img)
• Peax (img)
• CoolBox (fork of pyGenomeTracks) (img)

Ideogram

• eweitz/Ideogram (img)
• Ideogram (img)
• Ideoplot
• karyoploteR (img)
• KaryotypeSVG (img)
• NCBI Genome Decoration (img)
• UCSC Genome Graphs (img)
• genomegraphs (img)
• IdeoViz (img)
• Flash Gviewer (img)
• Ideogram viewer (img)
• chromPlot (img)
• PhenoGram (Can be web server or download) (img)
• RIdeogram (img)

Mobile

• iGenomics (img)

Pangenome

• Pan-Tetris (img)
• Panacaea (img)
• Panache (img)
• panX (img)
• RPAN (3kricedb) (img)
• PGAP-X (img)
• PGV (img)
• Phandango (img)

Protein

• Protael (img)
• ProteinPaint (Not open source) (img)
• pViz (img)
• Aquaria (img)
• nightingale/protvista (Used on InterProScan website https://www.ebi.ac.uk/interpro/) (img)
• drawProteins (img)
• IBS (Illustrator for Biological Sequences) (img)
• PFAM generate_graphic (Also see guide here https://pfam.xfam.org/help#tabview=tab10) (img)
• Prosite/MyDomains (img)

Heatmap

• UCSC Xena (img)
• VIVA (img)

Repeats

• REPAVER (img)
• GraphAlignmentViewer (img)
• REViewer (See also GraphAlignmentViewer, similar look and from illumina also) (img)
• StainedGlass (img)

Historical

• Internet Contig Explorer (img)

QC

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

Methylation

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

Phylogenetics

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

Long reads

• methylartist (img)

Assembly

• vega (Mentioned in https://www.biorxiv.org/content/10.1101/2021.07.02.450883v1.full.pdf also note: vega standards for vertebrate genome annotation database) (img)
• MIRA (orig paper also describes mira here http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.23.7465&rep=rep1&type=pdf) (img)

Coverage

• wiggleplotr (img)
• Trackplot (suggests citing bwtool linked here) (img)

Splicing

• splicejam (img)
• Slinker (See also, clinker (gene fusion software)) (img)

Hi-C

• Plotgardener (img)
• gcMapExplorer (img)

Deadlink

• VAMP (img)
• CGH-Explorer (img)
• DNAVis (img)

BLAST

• SequenceServer (img)

Academic license

• Consed (img)

Local ancestry

• fineSTRUCTURE aka ChromoPainter (img)
• MOSAIC (img)

Variation

• snpit (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/

The website code is MIT