trimming only first adapter if multiple found, but not necessarily best alignment
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- Python
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Description
Hi,
Thank you for your continued development of Cutadapt -- often my go-to tool for processing different types of sequence datasets.
Now, I am trying to utilize multiple adapter trimming capabilities but was wondering about the following.
According to the manual, the best-matching adapter will be trimmed, which resorts to the first adapter for ties.
Now, I was hoping to do the following. Evaluate multiple adapters and then trim the first adapter that satisfies a given error rate etc. So, the trimmed adapter should not always be the best in terms of alignment score. This may not be implemented directly but is there a workaround to yield that results, in a single pass? Apologies if I am missing something obvious.
Thanks a lot.
Dieter
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
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Research direction
No source file or test is named in the issue. Start with the manual's description of multiple-adapter trimming, then reproduce how the best-matching adapter and ties are selected. Done means determining whether a single-pass error-rate-first behavior or a documented workaround is possible.
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
- Needs clarification
- Newbie friendliness
- 20/100