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)