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

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

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

36 Citations (Scopus)

Abstract

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×.

Original languageEnglish
Pages (from-to)2074-2075
Number of pages2
JournalBioinformatics
Volume25
Issue number16
DOIs
Publication statusPublished - Aug 2009

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