{"id":"W4414434422","doi":"10.1101/gr.280510.125","title":"Long-read reconstruction of many diverse haplotypes with devider","year":2025,"lang":"en","type":"article","venue":"Genome Research","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Division of Biological Infrastructure; Natural Sciences and Engineering Research Council of Canada; National Institute of Allergy and Infectious Diseases; National Human Genome Research Institute; National Institutes of Health; National Science Foundation","keywords":"Haplotype; Metagenomics; Allele; DNA sequencing; Genomics; De Bruijn graph; Deep sequencing; Nanopore sequencing; Coalescent theory","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000316635,0.00007989951,0.0001150984,0.0001116239,0.0001220984,0.0000129124,0.000163903,0.00006799205,0.00004235225],"category_scores_gemma":[0.00004260393,0.00006692759,0.00003781003,0.0001956444,0.0002519378,5.039157e-7,0.0002122435,0.00008643906,0.000008138329],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000167973,"about_ca_system_score_gemma":0.0001279814,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00007578857,"about_ca_topic_score_gemma":0.000130135,"domain_scores_codex":[0.9991857,0.00006575289,0.000124146,0.000250117,0.0001390682,0.0002352609],"domain_scores_gemma":[0.9993407,0.00002133155,0.00002890818,0.0002845133,0.0002878719,0.0000366665],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0003252269,0.00006345093,0.08660486,0.0001143592,0.0003500164,0.00000466914,0.0001032873,0.0001000794,0.8832297,0.0006713051,0.0004579175,0.0279751],"study_design_scores_gemma":[0.001764822,0.001408147,0.6214985,0.0001192808,0.00007620491,0.0000401908,0.001722448,0.00003168526,0.2611546,0.001459089,0.1102809,0.0004441885],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9891129,0.003331787,0.0004082643,0.0001591956,0.00006028252,0.0001906903,0.00002026395,0.000001554767,0.006715077],"genre_scores_gemma":[0.9952693,0.001088791,0.0007976583,0.00002149821,0.00006306898,0.00001985324,0.00001091342,0.000008943881,0.002719969],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6220751,"threshold_uncertainty_score":0.2729228,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03829051054062729,"score_gpt":0.322208316346857,"score_spread":0.2839178058062297,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}