Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA.
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Yik Y Teo;
Heng Li;
Satheesh Nair;
Gordon Dougan;
John Wain;
Julian Parkhill;
(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: 10.1093/bioinformatics/btp344
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/.
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