{"id":"W4391567550","doi":"10.1038/s41564-023-01598-2","title":"COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes","year":2024,"lang":"en","type":"article","venue":"Nature Microbiology","topic":"Bacteriophages and microbial interactions","field":"Environmental Science","cited_by":46,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Lawrence Livermore National Laboratory; Syncrude; Biological and Environmental Research; Natural Sciences and Engineering Research Council of Canada; Innovative Genomics Institute; U.S. Department of Energy","keywords":"Contiguity; Completeness (order theory); Genome; Cobra; Computational biology; Biology; Virology; Evolutionary biology; Genetics; Computer science; Gene; Programming language; Ecology; Mathematics","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":"codex-gemma-dda1882f352a","candidate_categories":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.0001107318,0.0001242954,0.000210549,0.00002399003,0.00008430297,0.00004214016,0.0002045204,0.0001908669,0.0009356631],"category_scores_gemma":[0.0000107888,0.00007667212,0.000076027,0.00008424892,0.0002626601,0.00008911161,0.0002220715,0.0003636911,0.00006746491],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003403586,"about_ca_system_score_gemma":0.00000916737,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005208393,"about_ca_topic_score_gemma":0.0003849702,"domain_scores_codex":[0.9992926,0.00007402855,0.0001700358,0.0002773441,0.00002302716,0.000162932],"domain_scores_gemma":[0.9995868,0.000175762,0.00005291632,0.000150721,0.000008612945,0.00002522196],"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":[0.00001322501,0.00001423397,0.0003449045,0.000007592445,0.00007853933,0.000003311767,0.0002008993,7.714652e-7,0.9922559,0.0005120211,0.00176293,0.004805674],"study_design_scores_gemma":[0.0002935859,0.00009436377,0.1064373,0.0000229381,0.0001305977,0.00009710197,0.000138889,0.00007018007,0.3673682,0.0006725991,0.5244301,0.0002441721],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9890206,0.008190487,0.0001078051,0.0008466631,0.0007067897,0.0001617915,0.0002667533,0.00002806149,0.0006709779],"genre_scores_gemma":[0.9984311,0.000146466,0.0003461445,0.0005248639,0.00005808098,0.000005157483,0.00005743159,0.000009715231,0.0004210669],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6248878,"threshold_uncertainty_score":0.9999776,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.004955693513790414,"score_gpt":0.2361736204079528,"score_spread":0.2312179268941623,"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."}}