{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001045334,0.00103674,0.0007040197,0.001469639,0.0005023975,0.001124006,0.001103523,0.001007168,0.002953774],"category_scores_gemma":[0.004233022,0.0007087435,0.001182805,0.001036252,0.0005515965,0.0009681097,0.001593652,0.00116287,0.001313698],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004142494,"about_ca_system_score_gemma":0.0008263509,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001918305,"about_ca_topic_score_gemma":0.007722497,"domain_scores_codex":[0.9994574,0.00009600409,0.00004109626,0.0002544693,0.0001142722,0.00003674421],"domain_scores_gemma":[0.998689,0.000678693,0.00009680972,0.000300671,0.00018127,0.00005352804],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.000928549,0.0003932703,0.02704835,0.001462303,0.001105598,0.001243036,0.001721301,0.1417862,0.2673839,0.01707741,0.02024999,0.5196],"study_design_scores_gemma":[0.0001699444,0.0002864686,0.005469602,0.00008852472,0.0001348575,0.0006484787,0.000434647,0.862512,0.07109112,0.02180656,0.0372404,0.0001173921],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.1048774,0.0007890112,0.8638254,0.0001997501,0.0001795004,0.0001300974,0.003713118,0.02379586,0.002489813],"genre_scores_gemma":[0.1265898,0.0001830917,0.8618456,0.0002203017,0.00001963349,0.0001880814,0.007297769,0.001760351,0.001895345],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.002953774,"threshold_uncertainty_score":0.009881318,"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."}}