{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002799548,0.0001460081,0.0002400376,0.0001267147,0.0001256163,0.00001453105,0.000386051,0.0001413194,0.00007181468],"category_scores_gemma":[0.0001156054,0.0001397582,0.0001066237,0.0002006605,0.0002089936,7.087378e-7,0.0004782374,0.0002102556,0.000004453337],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005175633,"about_ca_system_score_gemma":0.0003110003,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001033387,"about_ca_topic_score_gemma":0.00006638716,"domain_scores_codex":[0.9979785,0.0005435202,0.0002625724,0.0004052007,0.0002705984,0.0005395708],"domain_scores_gemma":[0.9988037,0.00007614351,0.00004738146,0.000501887,0.0004405995,0.0001302676],"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":[0.00004542914,0.0001252142,0.01125976,0.00002911503,0.0001505138,0.000007794355,0.0003304948,0.000007256544,0.9826763,0.001826734,0.00003616339,0.003505269],"study_design_scores_gemma":[0.000398625,0.001471892,0.4266691,0.00001903281,0.00003285471,0.00003424747,0.00112982,0.00007275633,0.5344819,0.0009365436,0.03443043,0.000322767],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9119543,0.001233713,0.007747469,0.00003771114,0.00006541347,0.0003072061,0.00004638958,0.000002759099,0.07860506],"genre_scores_gemma":[0.9116717,0.00087166,0.08678994,0.00002407099,0.00011533,0.0000600773,0.00002118273,0.00002638484,0.0004196629],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4481944,"threshold_uncertainty_score":0.5699173,"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."}}