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

@article{citeulike:4774373, 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/.}, author = {Holt, Kathryn E. and Teo, Yik Y. and Li, Heng and Nair, Satheesh and Dougan, Gordon and Wain, John and Parkhill, Julian}, citeulike-article-id = {4774373}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp344}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/16/2074}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19497932}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19497932}, doi = {10.1093/bioinformatics/btp344}, issn = {1460-2059}, journal = {Bioinformatics (Oxford, England)}, month = {August}, number = {16}, pages = {2074--2075}, posted-at = {2009-06-18 08:42:04}, priority = {2}, title = {Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA.}, url = {http://dx.doi.org/10.1093/bioinformatics/btp344}, volume = {25}, year = {2009} }

TY - JOUR ID - citeulike:4774373 L3 - citeulike-article-id:4774373 N2 - 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/. IS - 16 JF - Bioinformatics (Oxford, England) SN - 1460-2059 EP - 2075 TI - Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA. VL - 25 SP - 2074 AU - Holt, Kathryn AU - Teo, Yik AU - Li, Heng AU - Nair, Satheesh AU - Dougan, Gordon AU - Wain, John AU - Parkhill, Julian PY - 2009/08/15/ UR - http://dx.doi.org/10.1093/bioinformatics/btp344 ER -