Allow --revcomp to output original orientation reads
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- Dominant language
- Python
- Stars
- 587
- Forks
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- Avg merge
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- Merged PRs (30d)
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Description
Dear cutadapt,
following #220, we have a use case with reads coming out of the sequencer in both orientations. We do several cleaning steps including primer trimming with cutadapt using --revcomp to look for primers in both orientations. However, we would like to output reads in the original orientations, so as to not modify this information and be able to use it in our downstream analyses. Is this something that could be considered in a future version?
Thanks a lot in advance!
Leonor
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 tracing the existing --revcomp behavior and reviewing issue #220 to understand how orientation changes are currently handled. Define how primer trimming should detect both orientations while output reads retain their sequencer orientation, then identify the relevant tests and add coverage for both input orientations.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 25/100