Carlo Ferravante1,2,3, Domenico Memoli1, Domenico Palumbo1, Paolo Ciaramella2, Antonio Di Loria2, Ylenia D'Agostino1, Giovanni Nassa1, Francesca Rizzo1, Roberta Tarallo1, Alessandro Weisz4,5, Giorgio Giurato6. 1. Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Via S. Allende, 1, 84081, Baronissi, SA, Italy. 2. Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Delpino 1, 80137, Naples, Italy. 3. Genomix4Life, via S. Allende 43/L, 84081, Baronissi, SA, Italy. 4. Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Via S. Allende, 1, 84081, Baronissi, SA, Italy. aweisz@unisa.it. 5. CRGS - Genome Research Center for Health, University of Salerno Campus of Medicine, 84081, Baronissi, SA, Italy. aweisz@unisa.it. 6. Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Via S. Allende, 1, 84081, Baronissi, SA, Italy. ggiurato@unisa.it.
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.
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.
Authors: Amanda Baizan-Edge; Peter Cock; Stuart MacFarlane; Wendy McGavin; Lesley Torrance; Susan Jones Journal: J Gen Virol Date: 2019-01-24 Impact factor: 3.891
Authors: Charles Mitchell; Julio A Polanco; Laura DeWald; Dustin Kress; Luc Jaeger; Wade W Grabow Journal: Nucleic Acids Res Date: 2019-07-09 Impact factor: 16.971