Opened 2 months ago
Last modified 8 weeks ago
#1613 closed enhancement
Include FastQ Screen in the demux step — at Initial Version
| Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
|---|---|---|---|
| Priority: | major | Milestone: | Reggie v5.3 |
| Component: | net.sf.basedb.reggie | Keywords: | |
| Cc: |
Description
FastQ Screen (https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) can be used to detect that sequences matches the expected organism.
We should include this as a QC step that is part of the regular demux step and also in the FASTQ import step for RNAseq data. Maybe we can also implement it for the WGS import step.
To begin with, we should use the default configuration of databases (see attached image).
We probably want to check the results and issue warnings, etc. Details has not yet been decided.
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