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Review
. 2021 Jul 5;22(Suppl 7):106.
doi: 10.1186/s12859-021-04004-y.

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

Carlo Ferravante #  1   2   3 , Domenico Memoli #  1 , Domenico Palumbo  1 , Paolo Ciaramella  2 , Antonio Di Loria  2 , Ylenia D'Agostino  1 , Giovanni Nassa  1 , Francesca Rizzo  1 , Roberta Tarallo  1 , Alessandro Weisz  4   5 , Giorgio Giurato  6
Affiliations
Review

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

Carlo Ferravante et al. BMC Bioinformatics. .

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.

Keywords: Next-Generation-Sequencing; Pipeline; Shotgun metagenomics.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
HOME-BIO workflow. The pipeline accepts NGS data as input and then proceeds to perform the analysis according to the different steps comprised in the three modules. The Quality Control module (in orange) performs QCs of the reads, low-complexity reads removal, and host and contaminant sequencing reads filtering (indicated in the dark orange rectangle), generating as output quality reports and graphical charts (indicated in the light orange rectangle). The sequence reads maintained after this step are processed using the Metagenomic shotgun module (in green) and/or the Assembly de novo module (in blue). In the first case, the reads are processed by Kraken2 and Kaiju (indicated in the dark green rectangle), producing as output text tables and charts. The Assembly de novo module processes the sequences by assembling with SPAdes and annotating with Kraken2 (dark blue rectangle), generating as output text tables and charts. For both modules, a custom database (indicates in the grey box) is used
Fig. 2
Fig. 2
Pie Charts regarding Bacteria, Viruses, and Protozoa detected in the samples. Pie-charts summarizing the percentage of Bacteria, Viruses, and Protozoa detected in samples SRR1206003 (Case) and SRR1202227 (Control) obtained by data analysis with the HOME-BIO pipeline
See this image and copyright information in PMC

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