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JBrowse is a genome browser which is web-based (as opposed to genome browsers such as Artemis and IGV which are stand-alone applications).

It was designed as a fast version of GBrowse,the well-known web-based UCSD genome browser. The key to its speed is Javascript language in which it was developed and which explains the J in its name.


Like other browsers, JBrowse simply gives a visual way of navigating a set of sequences.

  • Beside the magnifying glass icon, one can just the scaffolds one would liek seelcted as main reference sequence.

Installation notes

  • Available as subdir within apache root dir

First get reference sequence up

bin/prepare-refseqs.pl --fasta ~/scafs0/eelScaffold32.fa

Then it will accept GFF3 files (not GTF) files as feature tracks with this command:

bin/flatfile-to-json.pl --gff ~/scafs0/aug_s32_lp.gff --trackType CanvasFeatures --trackLabel aug_lp_s32

If you happen to have files in GTF, you can convert them to GFF3 with, say, Augustus' script in the following way:

~/swmake/augustus-3.2.2/scripts/gtf2gff.pl --printExon --gff3 < aug_s320_lp.gtf --out=aug_s320_lp.gff

BAM files can be incorporated with:

bin/add-bam-track.pl --label WTIPbam --bam_url WTIP_srtd.bam


  • The 2016 Genome Biology paper describing JBrowse, with a good description of the user interface.
  • The new official JBrowse FAQ.
  • Using JBrowse will mean knowing your file formats, so here is UCSC's definitions.