JBrowse

Introduction

Quick Javascript based Genome Viewer

Using

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.

Install

• 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 (note 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