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metagWGS

Introduction

metagWGS is a Nextflow bioinformatics analysis pipeline used for metagenomic Whole Genome Shotgun sequencing data (Illumina HiSeq3000 or NovaSeq, paired, 2*150bp).

Pipeline graphical representation

The workflow processes raw data from .fastq or .fastq.gz inputs and do the modules represented into this figure:

metagWGS steps

metagWGS is splitted into different steps that correspond to different parts of the bioinformatics analysis:

A report html file is generated at the end of the workflow with MultiQC.

The pipeline is built using Nextflow, a bioinformatics workflow tool to run tasks across multiple compute infrastructures in a very portable manner.

Three Singularity containers are available making installation trivial and results highly reproducible.

Documentation

metagWGS documentation is available here.

License

metagWGS is distributed under the GNU General Public License v3.

Copyright

2021 INRAE

Funded by

Anti-Selfish (Labex ECOFECT – N° 00002455-CT15000562) France Génomique National Infrastructure (funded as part of Investissement d’avenir program managed by Agence Nationale de la Recherche, contract ANR-10-INBS-09) With participation of SeqOccIn members financed by FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020.

Citation

metagWGS has been presented at JOBIM 2020:

Poster "Whole metagenome analysis with metagWGS", J. Fourquet, C. Noirot, C. Klopp, P. Pinton, S. Combes, C. Hoede, G. Pascal.

https://www.sfbi.fr/sites/sfbi.fr/files/jobim/jobim2020/posters/compressed/jobim2020_poster_9.pdf

metagWGS has been presented at JOBIM 2019 and at Genotoul Biostat Bioinfo day:

Poster "Whole metagenome analysis with metagWGS", J. Fourquet, A. Chaubet, H. Chiapello, C. Gaspin, M. Haenni, C. Klopp, A. Lupo, J. Mainguy, C. Noirot, T. Rochegue, M. Zytnicki, T. Ferry, C. Hoede.