motu-profiler

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

https://github.com/motu-tool/motus

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Repository

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

Basic Info

Host: GitHub
Owner: motu-tool
License: gpl-3.0
Language: Python
Default Branch: master
Size: 1.66 MB

Statistics

Stars: 156
Watchers: 10
Forks: 30
Open Issues: 5
Releases: 1

Created almost 8 years ago · Last pushed almost 2 years ago

Metadata Files

Readme License Citation

mOTU profiler

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)

doi: 10.1186/s40168-022-01410-z

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: * metaSNV v1.0.3, available also on bioconda (we assume metaSNV.py to be in the system path)

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

Installation

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: ```bash

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: ```bash

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

Basic examples

Here is a simple example on how to obtain a taxonomic profiling from a raw read file:

bash motus profile -s metagenomic_sample.fastq > taxonomy_profile.txt

You can separate the previous call as: bash 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:

bash 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:

shell 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: shell 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

How mOTUs works

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):

alt text

A mOTUs database is composed of three types of mOTUs: - ref-mOTUs, which represent known species, - meta-mOTUs, which represent unknown species obtained from metagenomic samples, - ext-mOTUs, which represent unknown species obtained from MAGs.

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): alt text

When profiling (motus profile) a metagenomic sample, the mOTUs tool maps the reads from the sample to the genes in the different mOTUs: alt text

ChangeLog

Version 3.1.0 2023-03-28 by AlessioMilanese * Improve database clustering algorithm and update the database (change the number of ext-mOTUs from 19,358 to 20,128)

Version 3.0.3 2022-07-13 by AlessioMilanese * Add command prep_long to allow the profiling of long reads (more information here)

Version 3.0.2 2022-01-31 by AlessioMilanese * Convert the repository to a python package and submit to PyPI

Version 3.0.1 2021-07-27 by AlessioMilanese * Improve ref-mOTUs taxonomy according to #76 * Solve bug with -A option

Version 3.0.0 2021-06-22 by AlessioMilanese * Improve code base * Minor bug fixes

Version 2.6.1 2021-04-27 by AlessioMilanese * Minor bug fixes * Improved the taxonomy of 32 ref-mOTUs (#45)

Version 2.6.0 2021-03-08 by AlessioMilanese * Add 19,358 new mOTUs * Add taxonomic profiles of > 11k metagenomic and metatranscriptomic samples. The updated merge function can integrate those in to the users results. * Minor bug fixes * Change -1 to unassigned

Version 2.5.1 2019-08-17 by AlessioMilanese * Update the taxonomy to participate to the CAMI 2 challenge

Version 2.5.0 2019-08-09 by AlessioMilanese * Add -db option to use a database from another directory * Add -A to print all taxonomy levels together * Update the database with more than 60k new reference genomes. There are 11,915 ref-mOTUs and 2,297 meta-mOTUs.

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.

Owner

Name: motu-tool
Login: motu-tool
Kind: organization

Repositories: 7
Profile: https://github.com/motu-tool

Citation (CITATION.cff)

cff-version: 1.2.0
message: If you use this software, please cite it as below.
title: 'Microbial abundance, activity and population genomic profiling with mOTUs2'
doi: 10.1038/s41467-019-08844-4
authors:
  - given-names: Alessio
    family-names: Milanese
    affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
    orcid: https://orcid.org/0000-0002-7050-2239
  - given-names: Daniel R.
    family-names: Mende
    affiliation: Daniel K. Inouye Center for Microbial Oceanography Research and Education, University of Hawaii at Mānoa, Honolulu, United States
    orcid: https://orcid.org/0000-0001-6831-4557
  - given-names: Lucas
    family-names: Paoli
    affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
      & Department of Biology, École normale supérieure, Paris, France
    orcid: https://orcid.org/0000-0003-0771-8309
  - given-names: Guillem
    family-names: Salazar
    affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
    orcid: https://orcid.org/0000-0002-9786-1493
  - given-names: Miguelangel
    family-names: Cuenca
    affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
    orcid: https://orcid.org/0000-0003-3435-9102
  - given-names: Pascal 
    family-names: Hingamp
    affiliation: Aix Marseille Univ, Université de Toulon, Marseille, France
  - given-names: Renato
    family-names: Alves
    affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
    orcid: https://orcid.org/0000-0002-7212-0234
  - given-names: Paul I.
    family-names: Costea
    affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
    orcid: https://orcid.org/0000-0003-1645-3947
  - given-names: Luis Pedro
    family-names: Coelho
    affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
    orcid: https://orcid.org/0000-0002-9280-7885
  - given-names: Thomas S. B.
    family-names: Schmidt 
    affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
    orcid: https://orcid.org/0000-0001-8587-4177
  - given-names: Alexandre 
    family-names: Almeida 
    affiliation: European Molecular Biology Laboratory, 
      European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK 
      & Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
    orcid: https://orcid.org/0000-0001-8803-0893
  - given-names: Alex L 
    family-names: Mitchell
    affiliation: European Molecular Biology Laboratory, 
      European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
  - given-names: Robert D.
    family-names: Finn
    affiliation: European Molecular Biology Laboratory, 
      European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
    orcid: https://orcid.org/0000-0001-8626-2148
  - given-names: Jaime 
    family-names: Huerta-Cepas
    affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
      & Centro de Biotecnología y Genómica de Plantas, 
      Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
    orcid: https://orcid.org/0000-0003-4195-5025
  - given-names: Peer 
    family-names: Bork
    affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
      & Max Delbrück Centre for Molecular Medicine, Berlin, Germany
      & Molecular Medicine Partnership Unit, Heidelberg, Germany
      & Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
    orcid: https://orcid.org/0000-0002-2627-833X
  - given-names: Georg
    family-names: Zeller
    affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
    orcid: https://orcid.org/0000-0003-1429-7485
  - given-names: Sunagawa
    family-names: Shinichi
    affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
    orcid: https://orcid.org/0000-0003-3065-0314

version: 3.0.3
date-released: 2022-07-13
repository-code: https://github.com/motu-tool/mOTUs
license: GNU General Public License v3.0
keywords:
- "Metagenomics"
- "Microbiome"
- "Software"
preferred-citation:
  type: article
  authors:
    - given-names: Alessio
      family-names: Milanese
      affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
      orcid: https://orcid.org/0000-0002-7050-2239
    - given-names: Daniel R.
      family-names: Mende
      affiliation: Daniel K. Inouye Center for Microbial Oceanography Research and Education, University of Hawaii at Mānoa, Honolulu, United States
      orcid: https://orcid.org/0000-0001-6831-4557
    - given-names: Lucas
      family-names: Paoli
      affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
        & Department of Biology, École normale supérieure, Paris, France
      orcid: https://orcid.org/0000-0003-0771-8309
    - given-names: Guillem
      family-names: Salazar
      affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
      orcid: https://orcid.org/0000-0002-9786-1493
    - given-names: Miguelangel
      family-names: Cuenca
      affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
      orcid: https://orcid.org/0000-0003-3435-9102
    - given-names: Pascal 
      family-names: Hingamp
      affiliation: Aix Marseille Univ, Université de Toulon, Marseille, France
    - given-names: Renato
      family-names: Alves
      affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
      orcid: https://orcid.org/0000-0002-7212-0234
    - given-names: Paul I.
      family-names: Costea
      affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
      orcid: https://orcid.org/0000-0003-1645-3947
    - given-names: Luis Pedro
      family-names: Coelho
      affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
      orcid: https://orcid.org/0000-0002-9280-7885
    - given-names: Thomas S. B.
      family-names: Schmidt 
      affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
      orcid: https://orcid.org/0000-0001-8587-4177
    - given-names: Alexandre 
      family-names: Almeida 
      affiliation: European Molecular Biology Laboratory, 
        European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK 
        & Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
      orcid: https://orcid.org/0000-0001-8803-0893
    - given-names: Alex L 
      family-names: Mitchell
      affiliation: European Molecular Biology Laboratory, 
        European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
    - given-names: Robert D.
      family-names: Finn
      affiliation: European Molecular Biology Laboratory, 
        European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
      orcid: https://orcid.org/0000-0001-8626-2148
    - given-names: Jaime 
      family-names: Huerta-Cepas
      affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
        & Centro de Biotecnología y Genómica de Plantas, 
        Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
      orcid: https://orcid.org/0000-0003-4195-5025
    - given-names: Peer 
      family-names: Bork
      affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
        & Max Delbrück Centre for Molecular Medicine, Berlin, Germany
        & Molecular Medicine Partnership Unit, Heidelberg, Germany
        & Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
      orcid: https://orcid.org/0000-0002-2627-833X
    - given-names: Georg
      family-names: Zeller
      affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
      orcid: https://orcid.org/0000-0003-1429-7485
    - given-names: Sunagawa
      family-names: Shinichi
      affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
      orcid: https://orcid.org/0000-0003-3065-0314
  doi: "10.1038/s41467-019-08844-4"
  journal: "Nature Communications"
  month: 3
  year: 2019
  title: "Microbial abundance, activity and population genomic profiling with mOTUs2"
  abstract: 'Metagenomic sequencing has greatly improved our ability to profile the composition 
  of environmental and host-associated microbial communities. However, the dependency of most methods 
  on reference genomes, which are currently unavailable for a substantial fraction of microbial species, 
  introduces estimation biases. We present an updated and functionally extended tool 
  based on universal (i.e., reference-independent), phylogenetic marker gene (MG)-based 
  operational taxonomic units (mOTUs) enabling the profiling of >7700 microbial species. 
  As more than 30% of them could not previously be quantified at this taxonomic resolution, 
  relative abundance estimates based on mOTUs are more accurate compared to other methods. 
  As a new feature, we show that mOTUs, which are based on essential housekeeping genes, 
  are demonstrably well-suited for quantification of basal transcriptional activity of community members. 
  Furthermore, single nucleotide variation profiles estimated using mOTUs reflect those from whole genomes, 
  which allows for comparing microbial strain populations (e.g., across different human body sites).'

GitHub Events

Total

Issues event: 26
Watch event: 10
Issue comment event: 28
Pull request event: 1
Fork event: 6

Last Year

Issues event: 26
Watch event: 10
Issue comment event: 28
Pull request event: 1
Fork event: 6

Committers

Last synced: over 1 year ago

All Time

Total Commits: 329
Total Committers: 12
Avg Commits per committer: 27.417
Development Distribution Score (DDS): 0.155

Past Year

Commits: 1
Committers: 1
Avg Commits per committer: 1.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Alessio Milanese	m**o@g**m	278
Renato Alves	a**c@g**m	18
Hans-Joachim Ruscheweyh	h**r@e**h	11
Lucas Paoli	l**i@g**m	8
Alessio Milanese	a**e@e**e	4
AlessioMilanese	a**m@K**h	3
SuShiAtGit	3****t	2
AlessioMilanese	a**m@m**h	1
Hans-Joachim Ruscheweyh (ID SIS)	h**r@b**h	1
Hans-Joachim Ruscheweyh	h**r@p**h	1
Florian Plaza Oñate	f****a	1
Valentyn Bezshapkin	6****z	1

Committer Domains (Top 20 + Academic)

pielou.ethz.ch: 1 bs-mbpr70.d.ethz.ch: 1 morgan.ethz.ch: 1 koch.ethz.ch: 1 embl.de: 1 ethz.ch: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 110
Total pull requests: 14
Average time to close issues: 7 months
Average time to close pull requests: about 7 hours
Total issue authors: 82
Total pull request authors: 6
Average comments per issue: 3.75
Average comments per pull request: 0.43
Merged pull requests: 11
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 11
Pull requests: 1
Average time to close issues: 3 months
Average time to close pull requests: N/A
Issue authors: 11
Pull request authors: 1
Average comments per issue: 0.73
Average comments per pull request: 0.0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

Jigyasa3 (7)
mikemc (6)
AlessioMilanese (5)
valentynbez (3)
zckoo007 (3)
Jibowe (2)
Anto007 (2)
sjaenick (2)
fplaza (2)
jzrapp (2)
sturne29 (2)
hjruscheweyh (2)
unode (2)
handibles (1)
trickovicmatija (1)

Pull Request Authors

AlessioMilanese (8)
unode (2)
matthpich (1)
lijier6 (1)
fplaza (1)
lijierr (1)
valentynbez (1)

Top Labels

Issue Labels

question (32) help wanted (19) enhancement (14) bug (12) next version (5) wontfix (1)

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Packages

Total packages: 1
Total downloads:
- pypi 37 last-month

Total dependent packages: 0
Total dependent repositories: 3
Total versions: 3
Total maintainers: 1

pypi.org: motu-profiler

Taxonomic profiling of metagenomes from diverse environments with mOTUs3

Homepage: https://github.com/motu-tool/mOTUs
Documentation: https://motu-profiler.readthedocs.io/
License: GPLv3
Latest release: 3.1.0
published almost 3 years ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 3
Downloads: 37 Last month

Rankings

Stargazers count: 6.3%

Forks count: 7.7%

Dependent repos count: 9.0%

Dependent packages count: 10.0%

Average: 12.7%

Downloads: 30.7%

Maintainers (1)

alessio.milanese

Last synced: 7 months ago

motu-profiler

Science Score: 67.0%

Repository

Basic Info

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Metadata Files

README.md

mOTU profiler

Pre-requisites

Installation

Install in the base environment

OR, create a new environment

Download and install mOTUs

Download the mOTUs database

Basic examples

How mOTUs works

ChangeLog

Owner

Citation (CITATION.cff)

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