5' adapter not trimmed if read ends early
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 587
- Forks
- 144
- Avg merge
- 2h 37m
- Merged PRs (30d)
- 1
Description
Given a sequence with 5' adapter, eg ALONGADAPTORsequence, if sequence is low quality in the end, or has polyG, cutadapt will trim this sequence into ALONGADAPTORseq (1st case) or ALONGADAP (2nd case). Then the -g argument and remove the adapter in the 1st case, but not in the 2nd case. And will cause adaptor contamination in the filtered reads.
Originally posted by @yech1990 in https://github.com/marcelm/cutadapt/issues/550#issuecomment-921100958
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 reproducing the two examples in the issue, using a 5' adapter with an early-ending low-quality or polyG read and the -g argument. Trace the adapter-trimming behavior and add coverage for the case where only part of the adapter remains; done means both examples remove the adapter without contamination in filtered reads.
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
- Mostly clear
- Newbie friendliness
- 42/100