{"doi":"10.1093/bioinformatics/btp344","title":"Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA","abstract":"<h4>Summary</h4>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.<h4>Availability</h4>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/.","journal":"Bioinformatics","year":2009,"id":4952,"datarank":0.5533319181170905,"base_score":3.6888794541139363,"endowment":3.6888794541139363,"self_citation_contribution":0.5533319181170905,"citation_network_contribution":0.0,"self_endowment_contribution":0.5533319181170905,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":39,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.0508,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2009-06-03","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1122,"name":"E. Shyong Tai","orcid":"0000-0003-2929-8966","position":1,"is_corresponding":false},{"id":30887,"name":"Alexandra P. Lewis","orcid":"0000-0002-6195-4786","position":2,"is_corresponding":false},{"id":50974,"name":"Satheesh Nair","orcid":"0000-0002-7297-1485","position":3,"is_corresponding":false},{"id":50975,"name":"Gordon Dougan","orcid":"0000-0003-0022-965X","position":4,"is_corresponding":false},{"id":50976,"name":"John Wain","orcid":"0000-0002-1257-1148","position":5,"is_corresponding":false},{"id":50977,"name":"Julian Parkhill","orcid":"0000-0002-7069-5958","position":6,"is_corresponding":false},{"id":21983,"name":"Harold Snieder","orcid":"0000-0003-1949-2298","position":7,"is_corresponding":false},{"id":1684,"name":"Kathryn E. Holt","orcid":"0000-0003-3949-2471","position":0,"is_corresponding":true}],"reference_count":9,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}