Default Min Mapping Quality

Microbial community profiling MetaPhlAn
1

Hello every one,
I was trying to find out what is the default min mapping quality used by metaphlan3. Could not find this in the documentation. The closest I got was to find out how to modify this value when running the program:

  --min_mapq_val MIN_MAPQ_VAL   Minimum mapping quality value (MAPQ)

Could you please enlight me? Thanks in advance.
David

2

Hi David,
The default MAPQ value used to filter alignments is 5

3

Got it! Thank you Francesco!