{"doi":"10.1101/2024.11.05.621838","title":"devider: long-read reconstruction of many diverse haplotypes","abstract":"Reconstructing haplotypes is important when sequencing a mixture of similar sequences. Long-read sequencing can connect distant alleles to disentangle similar haplotypes, but handling se-quencing errors requires specialized techniques. We present devider , an algorithm for haplotyping small sequences—such as viruses or genes—from long-read sequencing. devider uses a positional de Bruijn graph with sequence-to-graph alignment on an alphabet of informative alleles to provide a fast assembly-inspired approach compatible with various long-read sequencing technologies. On a synthetic Nanopore dataset containing seven HIV strains, devider recovered 97% of the haplotype content compared to 86% for the next best method while taking < 4 minutes and 1 GB of memory for > 8000× coverage. Benchmarking on synthetic mixtures of antimicrobial resistance (AMR) genes showed that devider recovered 83% of haplotypes, 23 percentage points higher than the next best method. On real PacBio and Nanopore datasets, devider recapitulates previously known results in seconds, disentan-gling a bacterial community with > 10 strains and an HIV-1 co-infection dataset. We used devider to investigate the within-host diversity of a long-read bovine gut metagenome enriched for AMR genes, discovering 13 distinct haplotypes for a tet(Q) tetracycline resistance gene with > 18, 000× coverage and 6 haplotypes for a CfxA2 beta-lactamase gene. We found clear recombination blocks for these AMR gene haplotypes, showcasing devider ’s ability to unveil ecological signals for heterogeneous mixtures.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":2054,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.048,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-11-08","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":23991,"name":"Christina Boucher","orcid":"0000-0001-9509-9725","position":1,"is_corresponding":false},{"id":23992,"name":"Yun William Yu","orcid":"0000-0002-8275-9576","position":2,"is_corresponding":false},{"id":23993,"name":"Noelle Noyes","orcid":"0000-0001-6149-1008","position":3,"is_corresponding":false},{"id":30887,"name":"Alexandra P. Lewis","orcid":"0000-0002-6195-4786","position":4,"is_corresponding":false},{"id":23990,"name":"Jim Shaw","orcid":"0000-0002-6990-7829","position":0,"is_corresponding":true}],"reference_count":61,"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":[]}