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

Holt, Kathryn E., Teo, Yik Y., Li, Heng, Nair, Satheesh, Dougan, Gordon, Wain, John and Parkhill, Julian (2009) Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA. Bioinformatics, 25 (16). pp. 2074-2075. ISSN 1367-4803

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Abstract

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 parameters, which afforded =80% sensitivity of SNP detection and strong correlation with true SNP frequency at poolwide read depth of 40×, declining only slightly at read depths 20–40×.

Item Type:	Article
Faculty \ School:	Faculty of Medicine and Health Sciences > Norwich Medical School
UEA Research Groups:	Faculty of Medicine and Health Sciences > Research Groups > Medical Microbiology (former - to 2018)
Depositing User:	Rhiannon Harvey
Date Deposited:	12 Jul 2011 11:15
Last Modified:	23 Oct 2022 01:49
URI:	https://ueaeprints.uea.ac.uk/id/eprint/33544
DOI:	10.1093/bioinformatics/btp344

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