ArticleBioinformatics (Oxford, England)2017
MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes.Briefings in bioinformatics · 2024Article
- Entourage: all-in-one sequence analysis software for genome assembly, virus detection, virus discovery, and intrasample variation profiling.BMC bioinformatics · 2024Article
- A Preliminary Study of the Potential Molecular Mechanisms of Individual Growth and Rumen Development in Calves with Different Feeding Patterns.Microorganisms · 2023Article
- Report of the third conference on next-generation sequencing for adventitious virus detection in biologics for humans and animals.Biologicals : journal of the International Association of Biological Standardization · 2023Article
- Enhanced Viral Metagenomics with Lazypipe 2.Viruses · 2023Article
- LABRADOR-A Computational Workflow for Virus Detection in High-Throughput Sequencing Data.Viruses · 2021Article
- Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics.Scientific reports · 2021Article
- Application of a bioinformatic pipeline to RNA-seq data identifies novel virus-like sequence in human blood.G3 (Bethesda, Md.) · 2021Article
- Tissue-associated microbial detection in cancer using human sequencing data.BMC bioinformatics · 2020Review
- Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types.Virus evolution · 2020Article
- A Modular Metagenomics Pipeline Allowing for the Inclusion of Prior Knowledge Using the Example of Anaerobic Digestion.Microorganisms · 2020Article
- No metagenomic evidence of tumorigenic viruses in cancers from a selected cohort of immunosuppressed subjects.Scientific reports · 2019Article
- Unbiased Taxonomic Annotation of Metagenomic Samples.Journal of computational biology : a journal of computational molecular cell biology · 2018Article
- Overview of Virus Metagenomic Classification Methods and Their Biological Applications.Frontiers in microbiology · 2018Review
- Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples.BMC genomics · 2017Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryShotgun 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. AVAILABILITY AND IMPLEMENTATION: https://github.com/bfosso/MetaShot. CONTACT: graziano.pesole@uniba.it. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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