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SnakeMAGs (Nachida Tadrent, Franck Dedeine, Vincent Hervé (Submitted). SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes. https://doi.org/10.5281/zenodo.7303463; https://github.com/Nachida08/SnakeMAGs) is a workflow for building MAGs (Metagenome Assembled Genomes) from raw Illumina metagenomic reads. During the test phase of the development of this tool, a comparative analysis with another workflow called ATLAS v2.9.1 (Kieser et al, 2020) was performed. To compare these two workflows, we analyzed ten publicly available termite gut metagenomes (accession numbers: SRR10402454; SRR14739927; SRR8296321; SRR8296327; SRR8296329; SRR8296337; SRR8296343; DRR097505; SRR7466794; SRR7466795) from five different studies : Waidele et al, 2019; Tokuda et al, 2018; Romero Victorica et al, 2020; Moreira et al, 2021; and Calusinska et al, 2020. In this repository, we provide the configuration files that were used to launch each of the workflows (SnakeMAGs_config.yaml and ATLAS_config.yaml), as well as the obtained results, i.e. the MAGs reconstructed from each metagenome and their taxonomic classification.