{"id":"W2951211878","doi":"10.1099/mgen.0.000116","title":"SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology","year":2017,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":162,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Centre for Disease Control; Dalhousie University; Simon Fraser University; Health Canada; University of Manitoba; Public Health Agency of Canada","funders":"Genome British Columbia; Genome Canada","keywords":"Phylogenomics; Indel; Computational biology; Genome; Whole genome sequencing; Scalability; Biology; Workflow; Genomics; Pipeline (software); Computer science; Genetics; Data mining; 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":[0.004156222,0.003173167,0.002657858,0.004544131,0.001436478,0.004142683,0.004218576,0.001966395,0.03316241],"category_scores_gemma":[0.0100109,0.002905038,0.004541973,0.003231277,0.0009023126,0.00366728,0.006061462,0.005039426,0.02655029],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001348129,"about_ca_system_score_gemma":0.004171405,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00734778,"about_ca_topic_score_gemma":0.01038501,"domain_scores_codex":[0.9978034,0.0005068828,0.0001982144,0.0006728822,0.0005302639,0.0002884451],"domain_scores_gemma":[0.9976058,0.001095324,0.0002815372,0.0004582098,0.0003405228,0.0002187199],"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":[0.002633942,0.0003882438,0.01514001,0.006471085,0.002692105,0.001484413,0.002659057,0.02099563,0.06928243,0.0166507,0.5647178,0.2968846],"study_design_scores_gemma":[0.00147982,0.0003896782,0.01779245,0.0008717716,0.0006758959,0.001328388,0.0004984763,0.238889,0.05828428,0.06233451,0.6164794,0.0009762653],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"software","genre_gemma":"methods","genre_scores_codex":[0.0065358,0.001544409,0.4175891,0.0006845296,0.000318254,0.0004908018,0.08810709,0.4804613,0.004268673],"genre_scores_gemma":[0.03670954,0.001219797,0.6702815,0.001117836,0.0001390645,0.001700288,0.2025909,0.08090473,0.005336374],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.03316241,"threshold_uncertainty_score":0.1109393,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03370385685354935,"score_gpt":0.2675280396315327,"score_spread":0.2338241827779834,"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."}}