Advance usage - motu-tool/mOTUs GitHub Wiki

Type motus for more information on the software.

To execute the motus profiler you need to call motus <command> [options]. The possible values for command are:

• profile, perform a taxonomic profiling (map_tax + calc_mgc + calc_motu);
• merge, append different profiles to create a table.

The profile command can be split in:

• map_tax, map reads to the marker gene database, and produce a SAM/BAM file;
• calc_mgc, aggregate reads from the same marker gene cluster (mgc) and it outputs the mgc abundance table. It uses the SAM/BAM file produced by map_tax;
• calc_motu, from a mgc abundance table (created by calc_mgc), produce the mOTUs abundance table;

To more information on the CAMI format and which parameters to use, check here.