marcelm / marcelm/cutadapt

trimming only first adapter if multiple found, but not necessarily best alignment

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Dominant language
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

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First steps

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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

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