The mOTU profiler is a computational tool that estimates relative taxonomic abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data.
Check the wiki for more information.
If you use mOTUs, please cite:
Reference genome-independent taxonomic profiling of microbiomes with mOTUs3
Hans-Joachim Ruscheweyh, Alessio Milanese, Lucas Paoli, Nicolai Karcher, Quentin Clayssen, Marisa Isabell Metzger, Jakob Wirbel, Peer Bork, Daniel R. Mende, Georg Zeller# & Shinichi Sunagawa#
Microbiome (2022)
The mOTU profiler requires:
In order to use the command snv_call
you need:
Check installation wiki to see how to install the dependencies with conda.
mOTUs can be installed either by using pip
or via conda
.
Installation with conda
has the advantage that it will also download and install dependencies:
# Install in the base environment
conda install motus
# OR, create a new environment
conda create -n motu-env motus
conda activate motu-env
Installation with pip
:
# Download and install mOTUs
pip install motu-profiler
# Download the mOTUs database
motus downloadDB
You can test that motus is intalled correctly with:
motus profile --test
Here is a simple example on how to obtain a taxonomic profiling from a raw read file:
motus profile -s metagenomic_sample.fastq > taxonomy_profile.txt
You can separate the previous call as:
motus map_tax -s metagenomic_sample.fastq -o mapped_reads.sam
motus calc_mgc -i mapped_reads.sam -o mgc_ab_table.count
motus calc_motu -i mgc_ab_table.count > taxonomy_profile.txt
rm mapped_reads.sam mgc_ab_table.count
The use of multiple threads (-t
) is recommended, since bwa will finish faster. Here is an example with Paired-End reads:
motus profile -f for_sample.fastq -r rev_sample.fastq -s no_pair.fastq -t 6 > taxonomy_profile.txt
You can merge taxonomy files from different samples with mOTU merge
:
motus profile -s metagenomic_sample_1.fastq -o taxonomy_profile_1.txt
motus profile -s metagenomic_sample_2.fastq -o taxonomy_profile_2.txt
motus merge -i taxonomy_profile_1.txt,taxonomy_profile_2.txt > all_sample_profiles.txt
You can profile samples that have been sequenced through different runs:
motus profile -f sample1_run1_for.fastq,sample1_run2_for.fastq -r sample1_run1_rev.fastq,sample1_run2_rev.fastq -s sample1_run1_single.fastq > taxonomy_profile.txt
The mOTUs tool performs taxonomic profiling of metagenomics and metatrancriptomics samples, i.e. it identifies species and their relative abundance present in a sample. It is based on a set of mOTUs (~species) contained in the mOTUs database. The mOTUs database is created from reference genomes, metagenomic samples and metagenome assembled genomes (MAGs):
A mOTUs database is composed of three types of mOTUs:
Note that meta- and ext-mOTUs will not have a species level annotation.
The mOTUs database is updated periodically, e.g the latest version (3.0.3), which doubles the number of profilable species by including ~600,000 draft genomes. Major releases are represented in the following graph (where the numbers represents the number of mOTUs for each of the three groups, with the same color-code as the previous graph):
When profiling (motus profile
) a metagenomic sample, the mOTUs tool maps the reads from the sample to the genes in the different mOTUs:
Version 3.1.0 2023-03-28 by AlessioMilanese
Version 3.0.3 2022-07-13 by AlessioMilanese
prep_long
to allow the profiling of long reads (more information here)Version 3.0.2 2022-01-31 by AlessioMilanese
Version 3.0.1 2021-07-27 by AlessioMilanese
-A
optionVersion 3.0.0 2021-06-22 by AlessioMilanese
Version 2.6.1 2021-04-27 by AlessioMilanese
Version 2.6.0 2021-03-08 by AlessioMilanese
-1
to unassigned
Version 2.5.1 2019-08-17 by AlessioMilanese
Version 2.5.0 2019-08-09 by AlessioMilanese
Version 2.1.1 2019-03-04 by AlessioMilanese
Version 2.1.0 2019-03-03 by AlessioMilanese
Version 2.0.1 2018-08-23 by AlessioMilanese
Version 2.0.0 2018-06-12 by AlessioMilanese
Version 2.0.0-rc1 2018-05-10 by AlessioMilanese