ArticlePeerJ2018
BLAST-based validation of metagenomic sequence assignments.
Article in PeerJ, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Harnessing probiotics to combat nonylphenol toxicity: a multiomics approach of gut microbiome remodelling in Silurus meridionalis.BMC genomics · 2026Article
- A framework of Microbial Genomic Database for clinical metagenomic pathogen diagnosis: development and multi-cohort evaluation.Frontiers in cellular and infection microbiology · 2026Article
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- Evaluation of DNA barcoding reference databases for marine species in the western and central Pacific Ocean.PeerJ · 2025Article
- Using nanopore sequencing to identify bacterial infection in joint replacements: a preliminary study.Briefings in functional genomics · 2024Article
- A global perspective on the abundance, diversity and mobility of antibiotic resistance genes inFrontiers in veterinary science · 2024Article
- Using nanopore sequencing to identify fungi from clinical samples with high phylogenetic resolution.Scientific reports · 2023Article
- Genome Characterisation of the CGMMV Virus Population in Australia-Informing Plant Biosecurity Policy.Viruses · 2023Article
- Benchmarking and Validation of a Bioinformatics Workflow for Meat Species Identification Using 16S rDNA Metabarcoding.Foods (Basel, Switzerland) · 2023Article
- Host metabolome and faecal microbiome shows potential interactions impacted by age and weaning times in calves.Animal microbiome · 2023Article
- MTSv: rapid alignment-based taxonomic classification and high-confidence metagenomic analysis.PeerJ · 2022Article
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- The microbial metabolite p-Cresol induces autistic-like behaviors in mice by remodeling the gut microbiota.Microbiome · 2021Article
- Transcriptomics of the Rooibos (Biotech (Basel (Switzerland)) · 2020Article
- Review
- Recentrifuge: Robust comparative analysis and contamination removal for metagenomics.PLoS computational biology · 2019Article
- Article
- Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
When performing bioforensic casework, it is important to be able to reliably detect the presence of a particular organism in a metagenomic sample, even if the organism is only present in a trace amount. For this task, it is common to use a sequence classification program that determines the taxonomic affiliation of individual sequence reads by comparing them to reference database sequences. As metagenomic data sets often consist of millions or billions of reads that need to be compared to reference databases containing millions of sequences, such sequence classification programs typically use search heuristics and databases with reduced sequence diversity to speed up the analysis, which can lead to incorrect assignments. Thus, in a bioforensic setting where correct assignments are paramount, assignments of interest made by "first-pass" classifiers should be confirmed using the most precise methods and comprehensive databases available. In this study we present a BLAST-based method for validating the assignments made by less precise sequence classification programs, with optimal parameters for filtering of BLAST results determined via simulation of sequence reads from genomes of interest, and we apply the method to the detection of four pathogenic organisms. The software implementing the method is open source and freely available.
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