Implement a new Hisat/Stringtie pipeline
|Reported by:||Nicklas Nordborg||Owned by:||Nicklas Nordborg|
The existing Hisat/Stringtie pipeline is getting old. There a newer versions of almost all programs that are used and there are also new versions of genome references.
It should be possible to run the new pipeline in parallel with the existing pipeline. The existing pipeline may be modified to save less data, but this remains to be decided.
The existing pipeline also include additional analysis step (eg. variant calling, SSP, etc) that may not be immediately available in the new pipeline.