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Articles by J. Parkhill
Total Records ( 1 ) for J. Parkhill
  K. E Holt , Y. Y Teo , H Li , S Nair , G Dougan , J Wain and J. Parkhill
 

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 40x, declining only slightly at read depths 20–40x.

 
 
 
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