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


BACKGROUND
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/.
Holt
Kathryn E
KE
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. kh2@sanger.ac.uk
Teo
Yik Y
YY
Li
Heng
H
Nair
Satheesh
S
Dougan
Gordon
G
Wain
John
J
Parkhill
Julian
J
D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000737:chemistry*; D030541:Databases, Genetic; D005787:Gene Frequency / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D012482:Salmonella paratyphi A / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
D004247:DNA