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I use Trim Galore which automatically recognizes adaptors.
https://github.com/FelixKrueger/TrimGalore
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There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
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Please check out [in this link.][1]
[1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
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[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
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I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
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I don't understand your comment. What do you mean?
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