Calc_motu

Type motus calc_motu to print the calc_motu options.

OPTIONS:

• -i (FILE), provide a mgc read count file (produced by calc_mgc). Example:

motus calc_motu -i mgc_reads.count > taxonomy.txt

• -n (STR), name of the sample
• -o (FILE), output file name, if you don't provide any file than it will print in stdout. This two calls produce the same result:

motus calc_motu -i mgc_reads.count > taxonomy.txt
motus calc_motu -i mgc_reads.count -o taxonomy.txt

• -e, profile only reference species (refOTUs).
• -B, print the taxonomy profile in BIOM format.
• -q, print the full rank taxonomy.
• -k (STR), taxonomy level. You can choose between [kingdom, phylum, class, order, family, genus, mOTU].
• -g (INT), number of marker genes cutoff. Given a mOTU, we calculate its abundance if at least -g marker genes have a read count different from 0. A value equal to 1 produce results with higher recall, while higher values produce results with higher precision. The minimum value is 1 and the maximum is 10, the default value is 3.
• -v (INT), verbose level: 1=error, 2=warning, 3=message, 4+=debugging. The default value is 3.
• -c, print result as counts instead of relative abundances.
• -p, print the NCBI id for every species.
• -C (STR), print result in CAMI format (BioBoxes format 0.9.1). Note that the mOTUs species definition and the NCBI species definition is not always congruent. As a result, you can decide three methods to save the result in CAMI format: "precision", where the discrepancies are deleted; "recall", where the relative abundances of the discrepancies are split and "parenthesis" where all the discrepancies are kept. Check The resulting profile page for more information and examples.