{"doi":"10.1186/gb-2009-10-3-r25","title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","abstract":"<jats:title>Abstract</jats:title><jats:p>Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" ext-link-type=\"uri\" xlink:href=\"http://bowtie.cbcb.umd.edu\">http://bowtie.cbcb.umd.edu</jats:ext-link>.</jats:p>","journal":"Genome Biology","year":2009,"id":12773,"datarank":1.5054665669677134,"base_score":10.036443779784754,"endowment":10.036443779784754,"self_citation_contribution":1.5054665669677134,"citation_network_contribution":0.0,"self_endowment_contribution":1.5054665669677134,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":22843,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.0509,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2009-03-04","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[],"reference_count":30,"raw_metadata":{"citation_network_status":"fetched"},"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":[]}