Using modified strobealign to align ancient DNA
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Description
Is your feature request related to a problem? Please describe
This is a request to make sure I or LLM I used are not hallucinating.
Describe the solution you'd like
I started investigating if strobealign could be used to align ancient DNA and after a while decide to use LLM (Claude Code) to automate my testing process and I decided to feed different papers + bwa's source code to it. The results are here:
https://github.com/teepean/strobealign/tree/aDNA
strobealign-ancient-multik.sh is used to perform the alignment. The sample I used was processed with adapterremoval before aligning. I decided to post the current results now.
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 reviewing the linked strobealign aDNA branch and its strobealign-ancient-multik.sh script, then compare the reported approach with the cited papers and BWA source code. Use the SAMEA117657086 sample context to assess the alignment results; the issue does not define acceptance criteria beyond validating whether the approach is sound.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- bash
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100