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motus - a tool for marker gene-based OTU (mOTU) profiling
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mOTUs profiler

The mOTUs profiler is a computational tool that estimates relative abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data.

Check the wiki for more information.

If you are using mOTUs2, please cite:

Alessio Milanese, Daniel R Mende, Lucas Paoli, Guillem Salazar, Hans-Joachim Ruscheweyh, Miguelangel Cuenca, Pascal Hingamp, Renato Alves, Paul I Costea, Luis Pedro Coelho, Thomas S B Schmidt, Alexandre Almeida, Alex L Mitchell, Robert D Finn, Jaime Huerta-Cepas, Peer Bork, Georg Zeller & Shinichi Sunagawa. Microbial abundance, activity and population genomic profiling with mOTUs2; Nature Communications 10, Article number: 1014 (2019). doi: 10.1038/s41467-019-08844-4

Pre-requisites

The mOTU profiler requires:

  • Python 3 (or higher)
  • the Burrow-Wheeler Aligner v0.7.15 or higher (bwa)
  • SAMtools v1.5 or higher (link)

In order to use the command snv_call you need:

Check installation wiki to see how to install the dependencies with conda.

Installation

git clone https://github.com/motu-tool/mOTUs_v2.git
cd mOTUs_v2
python setup.py
python test.py
export PATH=`pwd`:$PATH

Note: in the following examples we assume that the python script motus is in the system path.

Simple examples

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

ChangeLog

Version 2.1.1 2019-03-04 by AlessioMilanese

  • Correct problem with samtools when installing with conda

Version 2.1.0 2019-03-03 by AlessioMilanese

  • Correct error '\t\t' when printing -C recall
  • Update database (gene coordinates)

Version 2.0.1 2018-08-23 by AlessioMilanese

  • Add -C to print the result in CAMI format (BioBoxes format 0.9.1)
  • Add -K to snv_call command to keep all the directories produced by metaSNV

Version 2.0.0 2018-06-12 by AlessioMilanese

  • Set relative abundances as default (instead of counts)
  • Add -B to print the result in BIOM format
  • Add test directory
  • Python2 is not supported anymore
  • Minor bug fixes

Version 2.0.0-rc1 2018-05-10 by AlessioMilanese

  • First release supporting all basic functionality.
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