Essentials in Metagenomics (Part II)

Abstract

With the development of high-throughput next generation sequencing technologies and the technical advances to generate high-quality sequencing data, the bottleneck in implementing metagenomics for economic and social purposes in Latin America has shifted from obtaining DNA sequences to post-sequencing data analysis. Latin American countries still face challenges to develop and implement strategies for local data processing and data mining due to the limited bioinformatics capacity. Although many large computing grids already exist, outsourcing analyses and computing is not always the best solution since data transfer requires significant bandwidth due to the file sizes, and more importantly, it limits the training of local researchers to perform cutting-edge bioinformatics. Therefore, developing learning material in data processing and analysis in metagenomics is critical to the formation of new highly-skilled bioinformaticians. The present document is a tutorial in essential aspects of metagenomics data processing (post- sequencing) which was structured based on an extensive literature review, with the goal of presenting the current bioinformatics tools and workflows for extracting relevant, biological information out of a large sequencing data set. This is the second of a two-part series of documents designed to provide the essential background (experimental and computational) for users to approach the field of metagenomics. Users will find an overview of the different bioinformatic analyses that are commonly performed in metagenomic studies, including quality control, decontamination, coverage estimation, assembly, recovery of MAGs (metagenome- assembled genomes), taxonomic and functional classification of reads and contigs, and strain- level comparative analysis, among many other relevant topics. Users will also find rich discussions on the advantages and limitations that the different tools and methods offer and will be provided with external links and websites where additional information can be found.