Quickstart#

Installing mOTUs#

The mOTUs profiler, written in Python 3 (>=3.12), can be executed on a 64-bit Linux or MacOS system. However, there are external dependencies that need to be pre-installed. These dependencies can be manually installed or, more conveniently, using the conda package manager.

mOTUs is available as a package in bioconda and can be installed in an isolated environment:

conda create -n mOTUs4 motus
conda activate mOTUs4

After installation, you can test whether the tool was installed correctly by executing:

motus --help

mOTUs is also available on GitHub and on PyPI. Note Additional download of the database (motus downloadMGDB) is necessary in case of installation with pip.

Profiling a single sample#

You can use the motus profile command to create a taxonomic profile from a metagenomic sample consisting of one or more fastq files. See the Tutorial for more detailed instructions with a specific example.

# Profiling with forward, reverse and unpaired reads
motus profile -f for_sample.fastq -r rev_sample.fastq -s no_pair.fastq -t 4 -n test_sample -o taxonomy_profile.txt

Option	Description
`-f`, `--forward`	Input path - Paired Forward: One or more gzipped FastQ/A files containing forward reads. The input files must have the same order for both forward and reverse.
`-r`, `--reverse`	Input path - Paired Reverse: One or more gzipped FastQ/A files containing reverse reads. The input files must have the same order for both forward and reverse.
`-s`, `--single`	Input path - Single: One or more gzipped FastQ/A files. The order of the input files does not matter for single-end files.
`-o`, `--output-file`	Output prefix: Path to the output files. This prefix is also used for intermediate files.
`-n`, `--sample-name`	Sample name: Name of the sample. Required when merging samples. The default value is `unnamed sample`.
`-t`, `--threads`	Threads: Number of threads to use for the alignment step. Default is `1`.

To fine-tune the algorithm parameters (e.g., precision and recall) and modify the result format, refer to the Tutorial and Option manual.

Merging multiple profiles#

Using the motus merge command, you can easily merge the profiles of multiple samples:

# Merging profiles of sample A and sample B
motus merge -i sampleA.motus,sampleB.motus -o merged.motus

# Merging all profiles within a directory DIR
motus merge -d DIR -o merged.motus

Note

For a more comprehensive tutorial with practical examples, visit the Tutorial and Option manual.

mOTUs is part of SIB's portfolio of open tools and databases.

mOTUs is part of the ELIXIR-CH Service Delivery Plan.