Reconstruction of prokaryotic genomes from ten termite gut metagenomes using two distinct workflows: SnakeMAGs and ATLAS.
Authors/Creators
- 1. Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS - Université de Tours, 37200, Tours, France
- 2. Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS - Université de Tours, 37200, Tours, France & Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91120 Palaiseau, France
Description
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.
Files
MAGs_ATLAS.zip
Files
(60.7 MB)
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Additional details
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), 1–13
- 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–E12004
- Romero Victorica, M., Soria, M. A., Batista-García, R. A., Ceja-Navarro, J. A., Vikram, S., Ortiz, M., Ontañon, O., Ghio, S., Martínez-Ávila, L., Quintero García, 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), 1–14
- Moreira, E. A., Persinoti, G. F., Menezes, L. R., Paixão, D. A. A., Alvarez, T. M., Cairo, J. P. L. F., Squina, F. M., Costa-Leonardo, A. M., Rodrigues, A., Sillam-Dussès, 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), 1–12
- Calusinska, M., Marynowska, M., Bertucci, M., Untereiner, B., Klimek, D., Goux, X., Sillam-Dussès, 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), 1–12)