Paratyphi A SNP detection
Salmonella Paratyphi A diversity (test pool)
As of 2008, there were two finished genome sequences available for Salmonella Paratyphi A: ATCC9150 (EMBL:CP000026) and AKU_12601 (EMBL:FM200053). In this study, ATTC9150 and an additional 5 S. Paratyphi A isolates were sequenced using Illumina sequencing (one lane per isolate, 35 bp single-end reads, 20-40x read depth). Equal quantities of DNA from these 5 isolates plus ATCC9150 were pooled, and sequenced (Illumina sequencing, two lanes, 35 bp single-end reads). The data was used to develop a method for detecting SNPs and estimating their frequencies within pooled DNA samples, using the individual genome data to determine the expected frequency of each SNP in the pooled sample. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
"Holt et al, 2009. Bioinformatics, 25(16):2074-2075. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2722999/ 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 =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×. 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/."