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Using modified strobealign to align ancient DNA #1160

@teepean

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@teepean

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.

https://www.ebi.ac.uk/ena/browser/view/SAMEA117657086

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