Profile

The profile command perform a taxonomic profiling from reads in fastq format.

Type motus profile to print the profile options.

OPTIONS:

• -f (FILE), input file(s) for reads in forward orientation, fastq formatted. The file(s) can also be a ZIP file (.gz or .bz2)
• -r (FILE), input file(s) for reads in reverse orientation, fastq formatted. The file(s) can also be a ZIP file (.gz or .bz2). Example for forward and reverse reads analyzed in one lane:

motus profile -f for_sample.fastq -r rev_sample.fastq > taxonomic_profiling.txt

Example for forward and reverse reads analyzed in two lanes:

motus profile -f for_sample_lane1.fq,for_sample_lane2.fq -r rev_sample_lane1.fq,rev_sample_lane2.fq > taxonomic_profiling.txt

Note that the order of the files is important.

• -s (FILE), input file(s) for reads without mate, fastq formatted. The file(s) can also be a ZIP file (.gz or .bz2) You can analyze single read files alone:

motus profile -s sample_lane1.fq,sample_lane2.fq > taxonomic_profiling.txt

or together with forward and reverse reads:

motus profile -f for_sample_lane1.fq,for_sample_lane2.fq -r rev_sample_lane1.fq,rev_sample_lane2.fq -s sample_lane1.fq > taxonomic_profiling.txt

Note that in this last example we have only one single read for lane 1 and two lanes for for and rev.

• -n (STR), name of the sample
• -I (FILE), save the result of map_tax in .bam format. example:

motus profile -s sample.fq -I sample.bam > taxonomy.txt

• -i (FILE), provide a sam or bam input file, that you saved before with -I. example:

motus profile -i sample.bam > taxonomy.txt

• -M (FILE), save the mgc read counts table. example:

motus profile -s sample.fq -M mgc_read_count > taxonomy.txt

• -m (FILE), provide a mgc read count table, that you saved before with -M.example:

motus profile -m mgc_read_count > taxonomy.txt

• -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 profile -s sample.fq > taxonomy.txt
motus profile -s sample.fq -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 6, the default value is 3.
• -t (INT), number of threads to use when running bwa. It is suggested to use multiple threads, so that bwa will run faster.
• -v (INT), verbose level: 1=error, 2=warning, 3=message, 4+=debugging. The default value is 3.
• -y (STR), type of read counts that we use. Possible values: [base.coverage, insert.raw_counts, insert.scaled_counts].
• -c, print result as counts instead of relative abundances.
• -p, print the NCBI id.
• -l, minimum length of alignment for the reads (number of nucleotides). Default value is 75.
• -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.