Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA.
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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 > 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/.
SUBMITTER: Holt KE
PROVIDER: S-EPMC2722999 | biostudies-literature | 2009 Aug
REPOSITORIES: biostudies-literature
Publications
Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA.
Holt Kathryn E KE Teo Yik Y YY Li Heng H Nair Satheesh S Dougan Gordon G Wain John J Parkhill Julian J
Bioinformatics (Oxford, England) 20090603 16
<h4>Summary</h4>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 correlat ...[more]
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