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

BMC Bioinformatics

Paolo Ciaramella¹  Antonio Di Loria¹  Carlo Ferravante²  Domenico Memoli²  Giorgio Giurato²  Domenico Palumbo²  Roberta Tarallo²  Alessandro Weisz²  Francesca Rizzo²  Ylenia D’Agostino²  Giovanni Nassa² 

[1] Department of Veterinary Medicine and Animal Production, University of Naples Federico II;Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno;

关键词: Shotgun metagenomics;    Next-Generation-Sequencing;    Pipeline;   

DOI  :  10.1186/s12859-021-04004-y

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown