{"id":"W4405620286","doi":"10.1093/nargab/lqae176","title":"SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL), a Snakemate workflow for rapid and bulk analysis of Illumina sequencing of SARS-CoV-2 genomes","year":2024,"lang":"en","type":"article","venue":"NAR Genomics and Bioinformatics","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Ontario Institute for Cancer Research; Canada Research Chairs; Vector Institute; University of Saskatchewan; University of Manitoba; Public Health Agency of Canada; University Health Network; Health Sciences Centre; Sunnybrook Health Science Centre; University of Toronto; Dalhousie University; Perimeter Institute; McMaster University","funders":"Genome Canada; Canadian Institutes of Health Research; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University; University of Toronto; Natural Sciences and Engineering Research Council of Canada; McMaster University","keywords":"Workflow; Illumina dye sequencing; Whole genome sequencing; DNA sequencing; Genome; Personal genomics; Computer science; Computational biology; Biology; Genetics; Database; DNA; Gene","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":[0.003261157,0.001319699,0.0008916899,0.001305576,0.001103271,0.001735315,0.001207134,0.0007221901,0.01125014],"category_scores_gemma":[0.003674778,0.001247556,0.001628083,0.001157181,0.0004794053,0.0009885634,0.001854052,0.002418488,0.0136561],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005369656,"about_ca_system_score_gemma":0.001808334,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002926424,"about_ca_topic_score_gemma":0.007002568,"domain_scores_codex":[0.9980901,0.0003369141,0.0001624265,0.0006810917,0.0005820988,0.0001473807],"domain_scores_gemma":[0.9985943,0.0003637155,0.0001711727,0.0002872044,0.0004355482,0.0001480161],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.002337286,0.0002106112,0.009707727,0.001834577,0.0005387982,0.0006829679,0.001681669,0.007421254,0.4579982,0.01091376,0.2963023,0.2103708],"study_design_scores_gemma":[0.0004013343,0.0006863163,0.01277594,0.0003012369,0.0002028662,0.001018612,0.0002518706,0.07052416,0.3000699,0.009818411,0.6035073,0.0004419163],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.03080422,0.001067333,0.7941718,0.0006077948,0.0004459356,0.001300118,0.04981844,0.1039513,0.01783317],"genre_scores_gemma":[0.04198376,0.0005608923,0.8293557,0.0009090495,0.0001055919,0.002080908,0.0969687,0.01673815,0.01129738],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.01125014,"threshold_uncertainty_score":0.03763545,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05747356832884352,"score_gpt":0.3294186607319,"score_spread":0.2719450924030565,"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."}}