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; 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 DOI: https://doi.org/10.1093/bioinformatics/btp344

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 > or =80% sensitivity of SNP detection and strong correlation with true SNP frequency at poolwide read depth of 40x, declining only slightly at read depths 20-40x. AVAILABILITY: The method was implemented in Perl and relies on the opensource software Maq for read mapping and SNP calling. The Perl script is freely available from ftp://ftp.sanger.ac.uk/pub/pathogens/pools/.