Name
Title | ||
|---|---|---|
Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA |
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 ≥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/. Contact: kh2@sanger.ac.uk Supplementary information:Supplementary data are available at Bioinformatics online. |
Year | DOI | Venue |
|---|---|---|
2009 | 10.1093/bioinformatics/btp344 | Bioinformatics |
Keywords | Field | DocType |
allele frequency,dna,computational biology,high throughput,gene frequency | Population,Allele,Biology,Allele frequency,DNA,Single-nucleotide polymorphism,Bioinformatics,Genetics,SNP,Perl | Journal |
Volume | Issue | ISSN |
25 | 16 | 1367-4803 |
Citations | PageRank | References |
2 | 0.67 | 0 |
Authors | ||
7 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Kathryn E. Holt | 1 | 20 | 2.89 |
| Yik Y Teo | 2 | 30 | 6.81 |
| Heng Li | 3 | 3109 | 302.06 |
| S. Nair | 4 | 4 | 1.01 |
| Gordon Dougan | 5 | 2 | 1.00 |
| John Wain | 6 | 2 | 0.67 |
| Julian Parkhill | 7 | 291 | 35.97 |