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The mOTUs profiler is a computational tool that estimates relative abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data. The profiling method is based on ~100,000 universal single-copy marker genes that have been extracted from more than 3,000 metagenomic samples and ~25,000 reference genomes.

Installation

Look at Installation wiki for more information.

Taxonomic profiling of metagenomes and metatranscriptomes

1. Profile one sample;
2. Merge profiles into a table;
3. Explain the resulting profile;
4. Parameters to change the resulting profiles
5. Increase precision or recall
6. Advance usage

SNV calling

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

• map_snv, map reads to the marker gene database, and produce a BAM file suitable for metaSNV;
• snv_call, SNV calling using metaSNV;

Simple examples

The taxonomic profiling shown here can be executed with:

motus profile -f sample1.for.fastq -r sample1.rev.fastq -n sample1 -o s1.motu
motus profile -f sample2.for.fastq -r sample2.rev.fastq -s sample2.single.fastq -n sample2 -o s2.motu
motus merge -i s1.motu,s2.motu -o all_samples.motu

The SNV calling shown on the right can be executed with:

mkdir bam_files
motus map_snv -f sample1.for.fastq -r sample1.rev.fastq -o bam_files/s1.bam
motus map_snv -f sample2.for.fastq -r sample2.rev.fastq -s sample2.single.fastq -o bam_files/s2.bam
motus snv_call -d bam_files -o SNV_profiles

Taxonomic profiling

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;