{"id":"W4313491992","doi":"10.1111/tmi.13851","title":"<scp>Nano‐RECall</scp> provides an integrated pipeline for <scp>HIV</scp>‐1 drug resistance testing from Oxford Nanopore sequence data","year":2023,"lang":"en","type":"article","venue":"Tropical Medicine & International Health","topic":"HIV/AIDS drug development and treatment","field":"Medicine","cited_by":9,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"South African Medical Research Council; Medical Research Council; National Health Laboratory Service; National Cancer Institute; National Institutes of Health; Universiteit Stellenbosch","keywords":"Sanger sequencing; Nanopore sequencing; Amplicon; Minion; Drug resistance; Biology; HIV drug resistance; Computational biology; Mutation; DNA sequencing; Genetics; Polymerase chain reaction; Virology; Human immunodeficiency virus (HIV); Gene; Viral load","routes":{"ca_aff":true,"ca_fund":false,"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":[0.002482441,0.001137888,0.0007471126,0.001278479,0.0006925549,0.00164582,0.001463649,0.001051995,0.02076273],"category_scores_gemma":[0.004022425,0.0008963947,0.0006817852,0.0008073216,0.0005168395,0.00145836,0.001525248,0.0009747326,0.008014909],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009883614,"about_ca_system_score_gemma":0.001631913,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003770494,"about_ca_topic_score_gemma":0.01040014,"domain_scores_codex":[0.9986094,0.000138604,0.0001344401,0.0004021038,0.0006117515,0.0001036924],"domain_scores_gemma":[0.9967055,0.001001638,0.0004778939,0.0007225033,0.0009196184,0.0001729094],"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":[0.001452174,0.0001460893,0.02988726,0.001955996,0.0003204396,0.0007268893,0.0009505202,0.008734384,0.6124325,0.004801832,0.1051821,0.2334097],"study_design_scores_gemma":[0.0002030118,0.0004600784,0.02696652,0.000229389,0.0001494951,0.001600044,0.0002913434,0.07051788,0.693882,0.00366118,0.201753,0.0002860038],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.1695796,0.002351477,0.5649655,0.001680531,0.0003004886,0.001024292,0.07139657,0.1562206,0.03248095],"genre_scores_gemma":[0.2821326,0.0007778977,0.6198238,0.001330016,0.0001370087,0.001018864,0.07107358,0.009230203,0.01447603],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.02076273,"threshold_uncertainty_score":0.06945831,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1122291684586743,"score_gpt":0.3769453898817297,"score_spread":0.2647162214230555,"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."}}