Abstract
BackgroundNext-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.ResultsWe 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.ConclusionsHOME-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.
Highlights
Next-Generation-Sequencing (NGS) enables detection of microorganisms present in biological and other matrices of various origin and nature, allowing the identification of known phyla and strains and the discovery of novel ones
To test the performance of HOME-BIO, we considered the public dataset of Mitra et al [29], comprising 12 samples: 7 from symptomatic atherosclerotic plaques and 5 matched controls from asymptomatic atherosclerotic plaques
The analysis was performed running all three modules with default parameters and using the databases provided with the pipeline [42], comprising complete RefSeq bacterial, viral, and protozoa genome sequences and a subset of NCBI BLAST non-redundant database containing all proteins belonging to Archaea, Bacteria, and Viruses
Summary
We describe HOME-BIO, a user-friendly pipeline based on a dockerized solution, designed for analyzing shotgun metagenomic data avoiding time-consuming and errorprone installation and configuration steps. This modular pipeline provides a quality control step and the two main analysis approaches commonly used in metagenomic studies. Viral, protozoal, and protein databases, HOME-BIO generates an exhaustive taxonomic profiling of the biological entities in specimens. Project name: HOME-BIO Project home page: https://github.com/carlferr/HOME-BIO Operating system(s): Any Programming language: Python Other requirements: Docker License: GNU GPL Any restrictions to use by non-academics: none
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