{"id":"W4364353615","doi":"10.1002/cpz1.733","title":"ntLink: A Toolkit for <i>De Novo</i> Genome Assembly Scaffolding and Mapping Using Long Reads","year":2023,"lang":"en","type":"article","venue":"Current Protocols","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":55,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canada's Michael Smith Genome Sciences Centre","funders":"National Human Genome Research Institute; Canadian Institutes of Health Research; National Institutes of Health","keywords":"Scaffold; Sequence assembly; Computational biology; Genome; Computer science; Biology; Programming language; Genetics; Gene","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000371339,0.0001693546,0.000175699,0.00005925693,0.0001993489,0.00007160342,0.0001465784,0.00008364739,0.000001256408],"category_scores_gemma":[0.00006446492,0.0001725655,0.00008209917,0.000125403,0.00004483255,0.000001840356,0.000233123,0.00005385964,0.000003423249],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002153271,"about_ca_system_score_gemma":0.00007771694,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000001541513,"about_ca_topic_score_gemma":0.000002464702,"domain_scores_codex":[0.9988998,0.00002717467,0.0002193176,0.0003806205,0.00007647552,0.0003966091],"domain_scores_gemma":[0.9995182,0.00002121843,0.00008686584,0.0002199247,0.00007482121,0.00007900425],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00003609262,0.00002703853,0.009178855,0.0002772324,0.00004544772,0.000001505599,0.0001173877,0.0001480088,0.9826508,0.000071644,0.0002084585,0.00723753],"study_design_scores_gemma":[0.004618334,0.0008971323,0.06444452,0.0006851407,0.0001086431,0.00008576619,0.0003513462,0.004417997,0.2260958,0.001136793,0.6955089,0.001649639],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9704473,0.0007904628,0.007225848,0.0000500782,0.0001170187,0.02123737,0.00005080847,0.00001686834,0.00006427216],"genre_scores_gemma":[0.9302048,0.0003457936,0.004880354,0.0001095813,0.001131453,0.06291912,0.00013301,0.00008252241,0.0001933292],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.756555,"threshold_uncertainty_score":0.7037019,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.09019387454652054,"score_gpt":0.3647791775141179,"score_spread":0.2745853029675973,"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."}}