MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data

Bioinformatics
Bruno FossoGraziano Pesole

Abstract

Shotgun metagenomics by high-throughput sequencing may allow deep and accurate characterization of host-associated total microbiomes, including bacteria, viruses, protists and fungi. However, the analysis of such sequencing data is still extremely challenging in terms of both overall accuracy and computational efficiency, and current methodologies show substantial variability in misclassification rate and resolution at lower taxonomic ranks or are limited to specific life domains (e.g. only bacteria). We present here MetaShot, a workflow for assessing the total microbiome composition from host-associated shotgun sequence data, and show its overall optimal accuracy performance by analyzing both simulated and real datasets. https://github.com/bfosso/MetaShot. graziano.pesole@uniba.it. Supplementary data are available at Bioinformatics online.

Related Concepts

Classification
Virus
Workflow
Filamentous fungus
Nucleic Acid Sequencing
Bio-Informatics
Metagenomics
Computer Programs and Programming
Sequencing
Microbiome

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