Q: coverM compatible with bowtie2

[aistBMRG]

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]

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