Format

Send to

Choose Destination
Bioinformatics. 2009 Aug 15;25(16):2074-5. doi: 10.1093/bioinformatics/btp344. Epub 2009 Jun 3.

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

Author information

1
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. kh2@sanger.ac.uk

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/.

PMID:
19497932
PMCID:
PMC2722999
DOI:
10.1093/bioinformatics/btp344
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center