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wwood / CoverM

Read coverage calculator for metagenomics
GNU General Public License v3.0
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Q: coverM compatible with bowtie2 #171

Closed aistBMRG closed 1 year ago

aistBMRG commented 1 year ago

Thanks for developing this tool -- it is very helpful.

Now, just a small question. I performed alignments using bowtie2 and wanted to use coverm filter command to process the bam files produced by samtools. Just wanted to make sure that coverm is compatible with bowtie2, or may some flags by different compared to bwa-mem and minimap2. Would it be possible to clarify?

Thanks!

Dieter

wwood commented 1 year ago

Hi,

I believe it is compatible, yes. As always when running a tool new though, I'd suggest some sanity checking. Let me know if there's issues. Thanks, ben