Explain problems with pTrimmer
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- Dominant language
- Python
- Stars
- 21
- Forks
- 11
- Avg merge
- 12h 5m
- Merged PRs (30d)
- 24
Description
While testing pTrimmer for #552, I trimmed the ARTIC primers off of NCOV7-IL-Unknown_S34_L001_R1_001.fastq in the 20 Apr 2020 run. I found a bunch of differences between the cutadapt results and the pTrimmer results, and most of the differences looked better in the cutadapt results.
The performance of pTrimmer is much, much faster than cutadapt, so it's worth some effort to investigate these differences.
- Go through the differences and simplify the examples to see exactly what's causing those differences.
- Report issues on the pTrimmer project, if the examples are definitely incorrect.
- Try to offer fixes, if possible.
- Switch primer trimming from cutadapt to pTrimmer, if problems get fixed.
- See if adapter trimming is also possible with pTrimmer.
- See if censoring can be sped up with pTrimmer.
Contributor guide
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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 comparing cutadapt and pTrimmer outputs for NCOV7-IL-Unknown_S34_L001_R1_001.fastq from the 20 Apr 2020 run, then simplify the differences into reproducible examples. Determine which results are incorrect, report or fix pTrimmer issues where possible, and assess adapter trimming, primer-trimming replacement, and faster censoring.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100