{"doi":"10.1093/bioinformatics/btw152","title":"Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences","abstract":"<h4>Motivation</h4>Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10 kb in length, which have enabled high-quality genome assembly at an affordable cost. However, at present, long reads have an error rate as high as 10-15%. Complex and computationally intensive pipelines are required to assemble such reads.<h4>Results</h4>We present a new mapper, minimap and a de novo assembler, miniasm, for efficiently mapping and assembling SMRT and ONT reads without an error correction stage. They can often assemble a sequencing run of bacterial data into a single contig in a few minutes, and assemble 45-fold Caenorhabditis elegans data in 9 min, orders of magnitude faster than the existing pipelines, though the consensus sequence error rate is as high as raw reads. We also introduce a pairwise read mapping format and a graphical fragment assembly format, and demonstrate the interoperability between ours and current tools.<h4>Availability and implementation</h4>https://github.com/lh3/minimap and https://github.com/lh3/miniasm<h4>Contact</h4>hengli@broadinstitute.org<h4>Supplementary information</h4>Supplementary data are available at Bioinformatics online.","journal":"Bioinformatics","year":2016,"id":2490,"datarank":1.1162860092077438,"base_score":7.441906728051625,"endowment":7.441906728051625,"self_citation_contribution":1.1162860092077438,"citation_network_contribution":0.0,"self_endowment_contribution":1.1162860092077438,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1705,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.0435,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2016-03-19","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":30887,"name":"Alexandra P. Lewis","orcid":"0000-0002-6195-4786","position":0,"is_corresponding":true}],"reference_count":27,"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":[]}