DOI: 10.5281/zenodo.7334397
title: Reconstruction of prokaryotic genomes from ten termite gut metagenomes using two distinct workflows: SnakeMAGs and ATLAS.

description: <strong><em>SnakeMAGs</em></strong> (Nachida Tadrent, Franck Dedeine, Vincent Hervé (Submitted). <em>SnakeMAGs</em>: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes<em>.</em> 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 (<em>Kieser </em>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, <em>i.e. </em>the MAGs reconstructed from each metagenome and their taxonomic classification.
description: {"references": ["Kieser S, Brown J, Zdobnov EM, Trajkovski M, McCue LA. ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data. BMC Bioinformatics. 2020 Dec 22;21(1):257.", "Waidele, L., Korb, J., Voolstra, C. R., Dedeine, F., & Staubach, F. (2019). Ecological specificity of the metagenome in a set of lower termite species supports contribution of the microbiome to adaptation of the host. Animal Microbiome, 1(1), 1\u201313", "Tokuda, G., Mikaelyan, A., Fukui, C., Matsuura, Y., Watanabe, H., Fujishima, M., & Brune, A. (2018). Fiber-associated spirochetes are major agents of hemicellulose degradation in the hindgut of wood-feeding higher termites. Proceedings of the National Academy of Sciences of the United States of America, 115(51), E11996\u2013E12004", "Romero Victorica, M., Soria, M. A., Batista-Garc\u00eda, R. A., Ceja-Navarro, J. A., Vikram, S., Ortiz, M., Onta\u00f1on, O., Ghio, S., Mart\u00ednez-\u00c1vila, L., Quintero Garc\u00eda, O. J., Etcheverry, C., Campos, E., Cowan, D., Arneodo, J., & Talia, P. M. (2020). Neotropical termite microbiomes as sources of novel plant cell wall degrading enzymes. Scientific Reports, 10(1), 1\u201314", "Moreira, E. A., Persinoti, G. F., Menezes, L. R., Paix\u00e3o, D. A. A., Alvarez, T. M., Cairo, J. P. L. F., Squina, F. M., Costa-Leonardo, A. M., Rodrigues, A., Sillam-Duss\u00e8s, D., & Arab, A. (2021). Complementary Contribution of Fungi and Bacteria to Lignocellulose Digestion in the Food Stored by a Neotropical Higher Termite. Frontiers in Ecology and Evolution, 9(April), 1\u201312", "Calusinska, M., Marynowska, M., Bertucci, M., Untereiner, B., Klimek, D., Goux, X., Sillam-Duss\u00e8s, D., Gawron, P., Halder, R., Wilmes, P., Ferrer, P., Gerin, P., Roisin, Y., & Delfosse, P. (2020). Integrative omics analysis of the termite gut system adaptation to Miscanthus diet identifies lignocellulose degradation enzymes. Communications Biology, 3(1), 1\u201312)"]}