The latest JBrowse source (currently only in master branch) apparently supports CSI indexes for BAM and VCF files. If this is true, then we can think about the posibility of upgrading the reference sequence from the "parts" version to full-length pseudo molecules. However, there are downstream processing still affected by a lack of CSI index support including operations involving sambamba and GATK which do not support CSI (https://github.com/biod/sambamba/issues/284).
Tasks remaining:
[x] Upload full-pseudomolecule NGS data
[x] Upload reference-based tracks
[x] Add config files for NGS data
[x] Add config files for reference-based tracks
Add the following tracks as NCList, assuming this is still needed for search capabilities:
The latest JBrowse source (currently only in master branch) apparently supports CSI indexes for BAM and VCF files. If this is true, then we can think about the posibility of upgrading the reference sequence from the "parts" version to full-length pseudo molecules. However, there are downstream processing still affected by a lack of
CSIindex support including operations involvingsambambaandGATKwhich do not supportCSI(https://github.com/biod/sambamba/issues/284).Tasks remaining:
Add the following tracks as NCList, assuming this is still needed for search capabilities: