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Article

Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA.

Bioinformatics (Oxford, England) - 15 Aug 2009

Holt Kathryn E, Teo Yik Y, Li Heng, Nair Satheesh, Dougan Gordon, Wain John, Parkhill Julian

Abstract excerpt

SUMMARY: Here, we present a method for estimating the frequencies of SNP alleles present within pooled samples of DNA using high-throughput short-read sequencing. The method was tested on real data from six strains of the highly monomorphic pathogen Salmonella Paratyphi A, sequenced individually and in a pool. A variety of read mapping and quality-weighting procedures were tested to determine the optimal...

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Methodology Data sources Editorial policy Privacy About Contact Helena Bioinformatics

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Share to Polymorphism, Single Nucleotide

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Identifiers

PMID: 19497932
DOI: 10.1093/bioinformatics/btp344
PMCID: PMC2722999

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PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 5 Sept 2026. Manifest publication-graph-cohort-2026-09-05.1.

Source receipt: pubmed, retrieved 5 Sept 2026.

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