{"id":"W4391897827","doi":"10.1093/bioinformatics/btae066","title":"VariantDetective: an accurate all-in-one pipeline for detecting consensus bacterial SNPs and SVs","year":2024,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":10,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canadian Food Inspection Agency","funders":"Canadian Food Inspection Agency","keywords":"MIT License; Single-nucleotide polymorphism; Source code; Computational biology; Benchmarking; Pipeline (software); SNP; Biology; Computer science; Genetics; Data mining; Software; Gene; Genotype; Programming language","routes":{"ca_aff":true,"ca_fund":true,"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":[0.004562065,0.003077237,0.001727934,0.002819284,0.00169143,0.003166011,0.004445654,0.002218523,0.01616674],"category_scores_gemma":[0.0177508,0.001840573,0.002352041,0.00182075,0.0008603893,0.002261875,0.004225347,0.002646411,0.0134987],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008768849,"about_ca_system_score_gemma":0.002751589,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004970082,"about_ca_topic_score_gemma":0.008881574,"domain_scores_codex":[0.9966132,0.000547398,0.0002892058,0.001367221,0.0009003649,0.0002827273],"domain_scores_gemma":[0.9956566,0.002207648,0.0003567899,0.0008650268,0.000631989,0.000281904],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.004205602,0.0004597677,0.03245332,0.003026619,0.001970513,0.001904925,0.001294141,0.02063839,0.096051,0.01086308,0.3776603,0.4494723],"study_design_scores_gemma":[0.001428203,0.0006965146,0.02266818,0.0005018553,0.000829677,0.004604792,0.0005407138,0.4568245,0.1871829,0.04976547,0.2738507,0.001106508],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.01957784,0.00146579,0.5657493,0.0007437143,0.0006337637,0.0005831207,0.03767164,0.3695935,0.003981346],"genre_scores_gemma":[0.1087659,0.0006804995,0.7454042,0.001286423,0.0002283613,0.0009507646,0.09893975,0.03791064,0.005833444],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.01616674,"threshold_uncertainty_score":0.05408317,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03652047725925867,"score_gpt":0.285410330898393,"score_spread":0.2488898536391343,"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."}}