{"id":"W2112364185","doi":"10.1101/gr.186072.114","title":"CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","year":2015,"lang":"en","type":"article","venue":"Genome Research","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":12819,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Australian Research Council; Joint Genome Institute; Natural Sciences and Engineering Research Council of Canada; Great Barrier Reef Foundation; U.S. Department of Energy","keywords":"Biology; Genome; Metagenomics; Computational biology; Genetics; Gene","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":[0.006484275,0.001465642,0.00143557,0.00647225,0.0009334841,0.002478222,0.001874898,0.001669673,0.001099371],"category_scores_gemma":[0.02766071,0.0006144746,0.001547385,0.004399223,0.001097657,0.001630005,0.002945339,0.001019966,0.000701134],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009915772,"about_ca_system_score_gemma":0.0010981,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002254323,"about_ca_topic_score_gemma":0.002518323,"domain_scores_codex":[0.9945301,0.001108405,0.0005109461,0.001238194,0.002307075,0.0003051262],"domain_scores_gemma":[0.981239,0.008955953,0.004123622,0.002934195,0.00229082,0.000456442],"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":[0.002517794,0.0006383453,0.2940365,0.00381305,0.001365692,0.0007891693,0.001256851,0.06897219,0.3190466,0.00546158,0.009283709,0.2928187],"study_design_scores_gemma":[0.0001720709,0.001077059,0.1772199,0.0003053009,0.0003360871,0.001455822,0.0005259973,0.3672329,0.4293043,0.006944816,0.01507234,0.0003534734],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"methods","genre_scores_codex":[0.5033624,0.001813768,0.4621783,0.0002709342,0.0001020081,0.0005535998,0.02099021,0.008685307,0.002043372],"genre_scores_gemma":[0.5185885,0.0007013089,0.4415236,0.000175161,0.0000493375,0.0006895488,0.03663108,0.0009761828,0.0006652806],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.006484275,"threshold_uncertainty_score":0.03429252,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1745532526589507,"score_gpt":0.4126723215200291,"score_spread":0.2381190688610784,"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."}}