# Research Object Crate for MAGNETO (automated workflow dedicated to MAG reconstruction)

Original URL: https://workflowhub.eu/workflows/1815/ro_crate?version=4

MAGNETO is an automated snakemake workflow dedicated to MAG (Metagenome-Assembled Genomes) reconstruction from metagenomic data. It includes a fully-automated coassembly step informed by optimal clustering of metagenomic distances, and implements complementary genome binning strategies, for improving MAG recovery. # Key Features - **Quality Control (QC)**: Automatically assesses the quality and the contamination of input reads, ensuring that low-quality data are filtered out to improve downstream analyses. - **Assembly**: MAGNETO uses high-performance assembler to construct contigs from metagenomic reads. - **Gene Collection**: Extracts and compiles gene sequences from contigs, providing a comprehensive gene catalog directly after assembly. - **Binning**: Groups contigs into probable genomes using composition signatures and abundance profiles. - **Genomes collection**: Provides taxonomic and functional annotation of reconstructed MAGs. - **Metatranscriptomic mapping**: Mapping of transcriptomic reads on genes collection and/or MAGs obtained with previous analysis. # Documentation **Full description in the [wiki pages](https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto/-/wikis/home)** # Citing the pipeline Churcheward B, Millet M, Bihouée A, Fertin G, Chaffron S.
MAGNETO: An Automated Workflow for Genome-Resolved Metagenomics.
mSystems. 2022 Jun 15:e0043222. doi: [10.1128/msystems.00432-22](https://doi.org/10.1128/msystems.00432-22)

Author
  Samuel Chaffron, Audrey Bihouee, Hugo Lefeuvre
License
  GPL-3.0

## Contents

Main Workflow: MAGNETO (automated workflow dedicated to MAG reconstruction)
Size: 5912 bytes
Main Workflow Description: README.md
Size: 10848 bytes