Jbrowse2 Annelids

Description

This project intends to manage a Jbrowse2 deployment for annelid genomes in general and Platynereis dumerilii in particular.

Jbrowse2 is a genome browser with attractive features, notably that we can add tracks of interest corresponding to variations (VCFs), long read sequencing (GFFs from Pacbio), HI-C, ATACseq runs (BAM).

The publication reference is JBrowse 2: a modular genome browser with views of synteny and structural variation. Genome Biology (2023).

Access

Currently I use a branch based system to deploy resources using Gitlab. Here is what is available:

• https://genomes.arendt.embl.de : publicly available resources, from branch main
• https://genomes-dev.arendt.embl.de : some unpublished resources for internal lab use, from branch dev

Adding tracks

Go to the resources_to_s3_NF folder. There is Nextflow job (work in progress) that will process and upload to S3 the genomic tracks, and produce a new script to add the tracks to Jbrowse2. This scripts then goes to image/jbrowse_script.sh.

• genomes.csv spreadsheet for the assemblies
• tracks.csv for the genomic tracks to add.