Remove the "Incomplete adapter sequence" warning
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 587
- Forks
- 144
- Avg merge
- 2h 37m
- Merged PRs (30d)
- 1
Description
Cutadapt is used quite often to trim primer sequences, in which case it is expected that the "adapter" (primer) is not preceded/followed by a random nucleotide, but a specific one.
The warning was added to prevent people from providing an Illumina adapter that is missing the initial A. Instead, we could directly check for the Illumina adapter sequence (and only that one).
cf #779
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 locating the implementation of the "Incomplete adapter sequence" warning and read the related discussion in #779. Check how the Illumina adapter is identified; done means primer sequences with expected flanking bases no longer trigger the warning, while the missing-initial-A Illumina case remains covered.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100