BAM trimming according to primers with ivar, new rule

cbg-ethz / V-pipe

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

https://cbg-ethz.github.io/V-pipe/

Apache License 2.0

129 stars 43 forks source link

BAM trimming according to primers with ivar, new rule #113

Closed michalogit closed 1 year ago

michalogit commented 2 years ago

The rule is rather simple, works in my internal snakemake on Euler Fixed the problem I had with iVar, finding the -e switch, which outputs also reads that were not trimmed. This is not too logical in iVar, compared to other trimming software I've used. Added also in the same rule samtools sorting and indexing, copying your style from align.smk.

The pull request does not change anything in your files, just adds 3 files...

BioWu commented 2 years ago

Dose iVar ork well?

DrYak commented 2 years ago

Related tool that we might want to integrate as well:

https://github.com/nebiolabs/ampseer autodetection of amplicon.

Background:

since this pull request we created, we have now a mixture of different protocols in our cohort.

DrYak commented 1 year ago

integrated as of git commit 5154bbbd88208645086e96c67ffed5e5e8278ccd with working CI/CD

Currently in branch tribble, comming into branches and rubicon