{"id":"W2570111040","doi":"10.1101/092940","title":"SNVPhyl: A Single Nucleotide Variant Phylogenomics pipeline for microbial genomic epidemiology","year":2016,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":41,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Centre for Disease Control; University of British Columbia; Dalhousie University; Simon Fraser University; Health Canada; University of Manitoba; Public Health Agency of Canada","funders":"Genome British Columbia; Genome Canada","keywords":"Phylogenomics; Scalability; Computational biology; Genome; Whole genome sequencing; Workflow; Indel; Biology; Pipeline (software); Computer science; Data mining; Genetics; Phylogenetic tree; Single-nucleotide polymorphism; Database; Clade; Gene; Operating system","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":[0.004375861,0.002532016,0.002094786,0.004241029,0.001264061,0.003831173,0.004034476,0.001716541,0.03234147],"category_scores_gemma":[0.01117104,0.002304565,0.003427645,0.002926565,0.0008874747,0.003130257,0.004824677,0.00395791,0.02201504],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00130434,"about_ca_system_score_gemma":0.003594673,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.006838416,"about_ca_topic_score_gemma":0.006987194,"domain_scores_codex":[0.997777,0.000520756,0.0001980165,0.0007108868,0.0005545439,0.0002387555],"domain_scores_gemma":[0.9965917,0.001666355,0.000341023,0.0006085762,0.000527798,0.0002645904],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.002420421,0.0003332481,0.01507478,0.005568505,0.001922296,0.001054564,0.00171071,0.03110849,0.06026309,0.01836272,0.5893508,0.2728304],"study_design_scores_gemma":[0.001392188,0.0003164293,0.01408451,0.00077208,0.0005093114,0.0008850785,0.000386913,0.4156916,0.0829292,0.06550598,0.4167104,0.0008162964],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.007186914,0.0009263605,0.4070534,0.000718095,0.0002375763,0.0004379267,0.07418673,0.5058553,0.003397729],"genre_scores_gemma":[0.05500535,0.000728372,0.6857196,0.001017886,0.000145798,0.001612099,0.1735611,0.07776136,0.004448415],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.03234147,"threshold_uncertainty_score":0.108193,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02172959438046663,"score_gpt":0.232315305868616,"score_spread":0.2105857114881494,"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."}}