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

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