Metagenomics Bioinformatic Pipeline

• DOI: 10.1007/978-1-0716-2429-6_10
• Publication Date: 2022-07-11T16:08:00Z
• Authors: Diego Garfias-Gal...; Claudia Zirión-Ma...; Edder D. Bustos-Díaz; Tania Vanessa Are...; José Abel Lovaco-...; Aarón Espinosa-Jaime; J. Abraham Avelar...; Nelly Sélem-Mójica
• Keywords: Microbiota; Computational Biology; Metagenome; Metagenomics; Sequence Analysis, DNA; Software

Microbial communities' taxonomic and functional diversity has been broadly studied since sequencing technologies enabled faster and cheaper data obtainment. Nevertheless, the programming skills needed and the amount of software available may be overwhelming to someone trying to analyze these data. Here, we present a comprehensive and straightforward pipeline that takes shotgun metagenomics data through the needed steps to obtain valuable results. The raw data goes through a quality control process, metagenomic assembly, binning (the obtention of single genomes from a metagenome), taxonomic assignment, and taxonomic diversity analysis and visualization.