The bioBakery help forum

Parameters for short reads (100 bp)

I have new sequencing data from an MGI DNBSEQ-T7 machine with PE100 reads. I assume your default parameters are optimised for PE150? I found quite few species in my fecal samples, i.e. 50-100 species per sample and wonder whether I should tweak any parameters to optimise the profiling for shorter reads? Do you have suggestions?
Thanks a bunch!

Any suggestions are highly appreciated!

Hi Stef,
By default, MetaPhlAn filters out reads shorter than 75bp, so 100bp is not a problem. You can try to exclude the filtering by MAPQ by using --min_mapq_val -1, but I’d check the depth of sequencing