JBrowse

Typical commands used to set up a JBrowse

Author: Martijn Derks

• JBrowse is available for multiple species:
  • https://jbrowse.hpcagrogenomics.wur.nl/pig/
  • https://jbrowse.hpcagrogenomics.wur.nl/chicken/
  • https://jbrowse.hpcagrogenomics.wur.nl/cattle/
  • https://jbrowse.hpcagrogenomics.wur.nl/turkey/
• Users are free to add usefull commands to this tutorial

Install JBrowse

Download the latest JBrowse here: http://jbrowse.org/

Run the setup script to install perl dependencies and required modules

<source lang='bash'> unzip JBrowse-1.12.0.zip ./setup.sh </source>

Add reference sequence

bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa