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wwood / CoverM

Read coverage calculator for metagenomics
GNU General Public License v3.0
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Discussion/request: Read extraction for multiple references #220

Closed strejcem closed 2 months ago

strejcem commented 2 months ago

Hi,

I’m looking for a tool that can extract FASTQ reads mapped to multiple individual references, but specifically for long nanopore reads. Unfortunately, I haven’t been able to find any tool that supports long reads in this context. Essentially, I’m seeking functionality similar to BBsplit.sh, but compatible with long reads.

Would it be possible to extend coverm to support this?

Thank you! Michal

EDIT: Sorry for messing up the title and closing/opening

wwood commented 2 months ago

Hi @strejcem thanks for the thought, but I think this functionality is a bit far outside the current structure of CoverM at the moment. Perhaps in the future.