mutiple align reads and align parameter question question

[Sung-hub]

I am aligned Illumina pair end reads to a group of MAGs. Since these MAGs and illumina data were generated from Rumen microbiome WGS, there are many very highly similar species in the community. So, I am wondering how coverm treats the reads which align on the mutiple MAGs because sequence similarity/identity? does it count as both MAG coverage or just discard those mutilple aligned reads?

What are recommendations for the complex microbiome like rumen in terms of you align parameter (--min-read-aligned-percent, --min-read-percent-identity) to make sure reads align correctly?

[wwood]

Hi,

CoverM follows what the mapping software does, which is usually to arbirarily assign the read to one contig (the SAM format specifies that it must make a choice).

My recommendation is probably to dereplicate the genomes first, or use another tool which is better able to deal with closely related species.