{"id":"W2135361281","doi":"10.1101/gr.126599.111","title":"Assemblathon 1: A competitive assessment of de novo short read assembly methods","year":2011,"lang":"en","type":"article","venue":"Genome Research","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":539,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Cancer Agency","funders":"National Human Genome Research Institute; National Institute on Alcohol Abuse and Alcoholism; National Key Research and Development Program of China; National High-tech Research and Development Program; National Natural Science Foundation of China; Division of Emerging Frontiers; European Bioinformatics Institute; Howard Hughes Medical Institute; National Cancer Institute; National Institutes of Health; National Science Foundation","keywords":"Biology; Sequence assembly; Benchmark (surveying); Genome; Computational biology; Genomics; Contiguity; Hybrid genome assembly; Set (abstract data type); Computer science; Genetics; Gene; Transcriptome","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":["metaresearch"],"consensus_categories":[],"category_scores_codex":[0.07025234,0.004408376,0.003224634,0.006288171,0.003555082,0.006757162,0.007231326,0.005366192,0.007372495],"category_scores_gemma":[0.09267178,0.001580265,0.002847845,0.006076419,0.001702027,0.005682479,0.007751197,0.003674305,0.003172341],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.006160012,"about_ca_system_score_gemma":0.005156455,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.01089577,"about_ca_topic_score_gemma":0.01376019,"domain_scores_codex":[0.9373413,0.02604905,0.003402514,0.006942357,0.0233568,0.002908036],"domain_scores_gemma":[0.920871,0.03914776,0.002757322,0.009837645,0.02249009,0.004896101],"domain_codex":null,"domain_gemma":"methods","domain_candidate":"methods","domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.01403268,0.002629667,0.02238737,0.005014378,0.002487353,0.0006108556,0.00173946,0.1838971,0.02627586,0.03206328,0.1613392,0.5475228],"study_design_scores_gemma":[0.002067581,0.006592351,0.02119886,0.000837588,0.0006319649,0.0008954091,0.001077772,0.7485974,0.03511913,0.0297829,0.1525077,0.0006912955],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.4021207,0.0255418,0.4046677,0.008355553,0.004257556,0.003772985,0.02611424,0.03842219,0.0867473],"genre_scores_gemma":[0.3436665,0.004227772,0.5269417,0.001703902,0.0004901009,0.002518505,0.09250533,0.01572991,0.01221631],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.9297476,"threshold_uncertainty_score":0.3715343,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1601811763475329,"score_gpt":0.460701532668836,"score_spread":0.3005203563213031,"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."}}