nf-core / nf-core/seqinspector
Add SeqWho as alignment-free FastQScreen alternative
Open
Nobody has claimed this yet.
enhancement
- Dominant language
- Nextflow
- Stars
- 28
- Forks
- 44
- Avg merge
- 11d 8h
- Merged PRs (30d)
- 2
Description
Description of feature
SeqWho is another tool that allows to quickly corroborating the origin of sequencing reads, but in contrast to FastQScreen does not align to references, but uses a precomputed index and a classifier. Since there is also full support by MultiQC already, the tool could be a straightforward and useful addition to the pipeline.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reviewing how the pipeline currently integrates FastQScreen and how its MultiQC report is configured. Compare those entry points with SeqWho and its existing MultiQC support; done means SeqWho runs as an alignment-free alternative and appears correctly in the generated QC report.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100