{"doi":"10.1101/2022.12.23.521809","title":"mapquik: Efficient low-divergence mapping of long reads in minimizer space","abstract":"Abstract DNA sequencing data continues to progress towards longer reads with increasingly lower sequencing error rates. We focus on the critical problem of mapping, or aligning, low-divergence sequences from long reads (PacBio HiFi) to a reference genome, which poses challenges in terms of accuracy and computational resources when using cutting-edge read mapping approaches that are designed for all types of alignments. A natural idea would be to optimize efficiency with longer seeds to reduce the probability of extraneous matches; however, contiguous exact seeds quickly reach a sensitivity limit. We introduce mapquik , a novel strategy that creates accurate longer seeds by anchoring alignments through matches of k consecutively-sampled minimizers ( k -min-mers) and only indexing k -min-mers that occur once in the reference genome, thereby unlocking ultra-fast mapping while retaining high sensitivity. We demonstrate that mapquik significantly accelerates the seeding and chaining steps — fundamental bottlenecks to read mapping — for both the human and maize genomes with > 96% sensitivity and near-perfect specificity. On the human genome, mapquik achieves a 30× speed-up over the state-of-the-art tool minimap2 , and on the maize genome, a 350× speed-up over minimap2 , making mapquik the fastest mapper to date. These accelerations are enabled not only by minimizer-space seeding but also a novel heuristic 𝒪( n ) pseudo-chaining algorithm, which improves over the long-standing 𝒪( n log n ) bound. Minimizer-space computation builds the foundation for achieving real-time analysis of long-read sequencing data.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":302340,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.959,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":553654,"name":"Kristoffer Sahlin","orcid":"0000-0001-7378-2320","position":1,"is_corresponding":false},{"id":53921,"name":"Paul Medvedev","orcid":"0000-0003-3143-594X","position":2,"is_corresponding":false},{"id":3585,"name":"Bonnie Berger","orcid":"0000-0002-2724-7228","position":3,"is_corresponding":false},{"id":550281,"name":"Rayan Chikhi","orcid":"0000-0003-1099-8735","position":4,"is_corresponding":false},{"id":557253,"name":"Barış Ekim","orcid":"0000-0002-4040-403X","position":0,"is_corresponding":true}],"reference_count":44,"raw_metadata":null,"created_at":"2026-07-19T00:32:16.279991Z","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":[]}