MetaQuad: shared informative variants discovery in metagenomic samples.
Bioinform Adv
; 4(1): vbae030, 2024.
Article
en En
| MEDLINE
| ID: mdl-38476299
ABSTRACT
Motivation Strain-level analysis of metagenomic data has garnered significant interest in recent years. Microbial single nucleotide polymorphisms (SNPs) are genomic variants that can reflect strain-level differences within a microbial species. The diversity and emergence of SNPs in microbial genomes may reveal evolutionary history and environmental adaptation in microbial populations. However, efficient discovery of shared polymorphic variants in a large collection metagenomic samples remains a computational challenge. Results:
MetaQuad utilizes a density-based clustering technique to effectively distinguish between shared variants and non-polymorphic sites using shotgun metagenomic data. Empirical comparisons with other state-of-the-art methods show that MetaQuad significantly reduces the number of false positive SNPs without greatly affecting the true positive rate. We used MetaQuad to identify antibiotic-associated variants in patients who underwent Helicobacter pylori eradication therapy. MetaQuad detected 7591 variants across 529 antibiotic resistance genes. The nucleotide diversity of some genes is increased 6 weeks after antibiotic treatment, potentially indicating the role of these genes in specific antibiotic treatments. Availability and implementation MetaQuad is an open-source Python package available via https//github.com/holab-hku/MetaQuad.
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MEDLINE
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Revista:
Bioinform Adv
Año:
2024
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Article
País de afiliación:
China