{"id":"W3016821318","doi":"10.1093/bioinformatics/btaa253","title":"ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs","year":2020,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":44,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canada's Michael Smith Genome Sciences Centre","funders":"National Human Genome Research Institute; National Institutes of Health; Genome British Columbia; Genome Canada","keywords":"Sequence assembly; Computer science; Python (programming language); Reference genome; Synteny; Genome; Graph; Programming language; Theoretical computer science; Biology; 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":[0.00007946497,0.0001775792,0.0001828285,0.00003309863,0.0001331563,0.00005333835,0.0001249411,0.0001021059,0.000004912246],"category_scores_gemma":[0.00004174736,0.0001594716,0.00007221879,0.00009165742,0.00006330955,0.000002809143,0.000220331,0.00004522982,0.000007521076],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000005794504,"about_ca_system_score_gemma":0.00003678235,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000003773808,"about_ca_topic_score_gemma":0.000001600915,"domain_scores_codex":[0.9991782,0.00001344646,0.0003059833,0.0001707523,0.0001019039,0.0002296752],"domain_scores_gemma":[0.9995133,0.000008924712,0.000112518,0.0001692646,0.00005744842,0.000138602],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00005972403,0.00003338265,0.00909602,0.0002379674,0.000293645,0.000004219215,0.002311618,0.0003116547,0.9711359,0.0005384751,0.009474789,0.006502583],"study_design_scores_gemma":[0.004393051,0.001137702,0.007457113,0.0001135275,0.0003565923,0.000192208,0.00400653,0.1068093,0.7122891,0.0003622736,0.160586,0.002296648],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9938186,0.001028861,0.002462752,0.0002773816,0.000123365,0.0001609404,0.00002496415,0.000008465819,0.002094602],"genre_scores_gemma":[0.9652467,0.0004638872,0.03291629,0.00111042,0.0001765072,0.000004193972,0.00002009772,0.00002036893,0.0000415516],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2588468,"threshold_uncertainty_score":0.6503062,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03114288380858979,"score_gpt":0.2481334508236804,"score_spread":0.2169905670150906,"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."}}