{"id":"W4402348265","doi":"10.1186/s13073-024-01380-x","title":"Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses","year":2024,"lang":"en","type":"article","venue":"Genome Medicine","topic":"Bacteriophages and microbial interactions","field":"Environmental Science","cited_by":50,"is_retracted":false,"has_abstract":true,"ca_institutions":"Institute of Infection and Immunity","funders":"National Institute for Health and Care Research","keywords":"Metagenomics; Nanopore sequencing; Illumina dye sequencing; Computational biology; Workflow; Deep sequencing; DNA sequencing; Minion; Biology; Sequence assembly; Genome; Transcriptome; Bioinformatics; Computer science; Genetics; Gene","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":[],"consensus_categories":[],"category_scores_codex":[0.005072223,0.001356258,0.001009839,0.001883125,0.0004015491,0.001735988,0.000781461,0.001128972,0.0009520756],"category_scores_gemma":[0.003741304,0.0004163444,0.00159381,0.001134641,0.0005867953,0.001402432,0.001566687,0.0007220068,0.0003593997],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001478954,"about_ca_system_score_gemma":0.001050739,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001545198,"about_ca_topic_score_gemma":0.002894409,"domain_scores_codex":[0.9964071,0.001278284,0.0001725486,0.0007424895,0.001109202,0.0002903114],"domain_scores_gemma":[0.9978157,0.000804809,0.0003470901,0.0001610767,0.0006908855,0.0001804591],"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":[0.001567283,0.000485423,0.09687124,0.001881116,0.001253359,0.0001629366,0.0002301872,0.02266592,0.7715263,0.001355495,0.0005289126,0.1014718],"study_design_scores_gemma":[0.00008681717,0.006714242,0.1019825,0.0003970421,0.00154942,0.0007594061,0.0006912174,0.1282548,0.7454826,0.004253832,0.009648815,0.0001792641],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8507728,0.01180693,0.1284218,0.0006276247,0.0001468003,0.0009683719,0.002912735,0.0004442309,0.003898742],"genre_scores_gemma":[0.8209096,0.00410524,0.1699849,0.0003397742,0.00006296238,0.0005977169,0.002989026,0.00009920414,0.0009115346],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.005072223,"threshold_uncertainty_score":0.02682477,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1108215601092,"score_gpt":0.3325387943933779,"score_spread":0.2217172342841779,"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."}}