{"doi":"10.1101/2020.09.14.296525","title":"AFLAP: Assembly-Free Linkage Analysis Pipeline using <i>k</i> -mers from whole genome sequencing data","abstract":"Abstract Background Genetic maps are an important resource for validation of genome assemblies, trait discovery, and breeding. Next generation sequencing has enabled production of high-density genetic maps constructed with 10,000s of markers. Most current approaches require a genome assembly to identify markers. Our Assembly Free Linkage Analysis Pipeline (AFLAP) removes this requirement by using uniquely segregating k -mers as markers to rapidly construct a genotype table and perform subsequent linkage analysis. This avoids potential biases including preferential read alignment and variant calling. Results The performance of AFLAP was determined in simulations and contrasted to a conventional workflow. We tested AFLAP using 100 F 2 individuals of Arabidopsis thaliana , sequenced to low coverage. Genetic maps generated using k -mers contained over 130,000 markers that were concordant with the genomic assembly. The utility of AFLAP was then demonstrated by generating an accurate genetic map using genotyping-by-sequencing data of 235 recombinant inbred lines of Lactuca spp. AFLAP was then applied to 83 F 1 individuals of the oomycete Bremia lactucae , sequenced to &gt;5x coverage. The genetic map contained over 90,000 markers ordered in 19 large linkage groups. This genetic map was used to fragment, order, orient, and scaffold the genome, resulting in a much-improved reference assembly. Conclusions AFLAP can be used to generate high density linkage maps and improve genome assemblies of any organism when a mapping population is available using whole genome sequencing or genotyping-by-sequencing data. Genetic maps produced for B. lactucae were accurately aligned to the genome and guided significant improvements of the reference assembly.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":125368,"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":0.9452,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":571310,"name":"Lin Zhang","orcid":"0000-0001-6476-4526","position":1,"is_corresponding":false},{"id":571311,"name":"Juliana Gil","orcid":"0000-0002-9042-7459","position":2,"is_corresponding":false},{"id":571312,"name":"Rongkui Han","orcid":"0000-0001-9635-6922","position":3,"is_corresponding":false},{"id":571981,"name":"Keri Cavanaugh","orcid":null,"position":4,"is_corresponding":false},{"id":571313,"name":"Richard W. Michelmore","orcid":"0000-0002-7512-592X","position":5,"is_corresponding":false},{"id":571309,"name":"Kyle Fletcher","orcid":"0000-0003-1191-9939","position":0,"is_corresponding":true}],"reference_count":36,"raw_metadata":null,"created_at":"2026-07-18T23:15:15.482227Z","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":[]}