{"id":"W4413381394","doi":"10.3389/fgene.2025.1516791","title":"A Benchmark of methods for SARS-CoV-2 whole genome sequencing and development of a more sensitive method","year":2025,"lang":"en","type":"article","venue":"Frontiers in Genetics","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Centre hospitalier universitaire de Québec; McGill University; Université Laval; McGill Genome Centre","funders":"Canadian Institutes of Health Research; Compute Canada; Genome Canada","keywords":"Amplicon; Genome; Virology; Biology; Computational biology; Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); Coronavirus disease 2019 (COVID-19); Pandemic; Genetics; Polymerase chain reaction; Gene; Medicine; Infectious disease (medical specialty); Disease","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":[0.01608757,0.002451192,0.001627043,0.002850563,0.001483119,0.003024745,0.002477452,0.004358283,0.003787141],"category_scores_gemma":[0.02229959,0.001472793,0.002158517,0.001698911,0.001692861,0.002307416,0.002999216,0.004122954,0.004265394],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001356947,"about_ca_system_score_gemma":0.002298648,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001772813,"about_ca_topic_score_gemma":0.002845926,"domain_scores_codex":[0.9801248,0.006104735,0.001420677,0.004279308,0.007431705,0.0006387992],"domain_scores_gemma":[0.9870919,0.004872642,0.001108342,0.002371317,0.004133293,0.0004225511],"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":[0.0008947451,0.000487698,0.007053472,0.003405613,0.0004429347,0.0003982305,0.0009869492,0.01354479,0.7840194,0.008175572,0.008185722,0.172405],"study_design_scores_gemma":[0.0001083341,0.001225348,0.008662074,0.0006008249,0.0002429511,0.001437725,0.000456052,0.08332081,0.8205708,0.006293148,0.07669591,0.0003859543],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.04704792,0.006837221,0.9260201,0.0009701779,0.0006121899,0.001386131,0.003080511,0.007881061,0.006164659],"genre_scores_gemma":[0.05156099,0.001920079,0.933862,0.0006225749,0.0001002069,0.001635973,0.005301056,0.001617824,0.003379186],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01608757,"threshold_uncertainty_score":0.08508027,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05931018605642217,"score_gpt":0.422897577278417,"score_spread":0.3635873912219948,"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."}}