HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis

Autor: Carlo Ferravante, Domenico Memoli, Domenico Palumbo, Paolo Ciaramella, Antonio Di Loria, Ylenia D’Agostino, Giovanni Nassa, Francesca Rizzo, Roberta Tarallo, Alessandro Weisz, Giorgio Giurato
Jazyk: angličtina
Rok vydání: 2021
Předmět:
Zdroj: BMC Bioinformatics, Vol 22, Iss S7, Pp 1-10 (2021)
Druh dokumentu: article
ISSN: 1471-2105
DOI: 10.1186/s12859-021-04004-y
Popis: Abstract Background Next-Generation-Sequencing (NGS) enables detection of microorganisms present in biological and other matrices of various origin and nature, allowing not only the identification of known phyla and strains but also the discovery of novel ones. The large amount of metagenomic shotgun data produced by NGS require comprehensive and user-friendly pipelines for data analysis, that speed up the bioinformatics steps, relieving the users from the need to manually perform complex and time-consuming tasks. Results We describe here HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities), an exhaustive pipeline for metagenomics data analysis, comprising three independent analytical modules designed for an inclusive analysis of large NGS datasets. Conclusions HOME-BIO is a powerful and easy-to-use tool that can be run also by users with limited computational expertise. It allows in-depth analyses by removing low-complexity/ problematic reads, integrating the analytical steps that lead to a comprehensive taxonomy profile of each sample by querying different source databases, and it is customizable according to specific users’ needs.
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