{"id":"W4406376882","doi":"10.7717/peerj.18785","title":"Benchmarking of a time-saving and scalable protocol for the extraction of DNA from diverse viromes","year":2025,"lang":"en","type":"article","venue":"PeerJ","topic":"Bacteriophages and microbial interactions","field":"Environmental Science","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University","funders":"Fonds de Recherche du Québec - Santé; Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research","keywords":"Human virome; DNA extraction; Biology; Protocol (science); Computational biology; Microbiome; Norovirus; Bioinformatics; Metagenomics; Genetics; Medicine; Polymerase chain reaction; Virus","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":[0.007065374,0.001563687,0.001219923,0.00238656,0.001110463,0.002317657,0.001745332,0.001847878,0.002731021],"category_scores_gemma":[0.01098565,0.0006511702,0.001127056,0.001490269,0.001168043,0.001381497,0.002102633,0.001525727,0.003270065],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006777291,"about_ca_system_score_gemma":0.002006121,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00140222,"about_ca_topic_score_gemma":0.002851929,"domain_scores_codex":[0.9917836,0.002113623,0.0009720011,0.00165425,0.003041906,0.0004346026],"domain_scores_gemma":[0.9949358,0.001477173,0.0006447124,0.0008256132,0.001777736,0.0003389056],"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":[0.0003571379,0.0003685332,0.002284633,0.0008220532,0.00008180447,0.0001510823,0.0003223791,0.00156525,0.9652429,0.0003589297,0.001078602,0.02736675],"study_design_scores_gemma":[0.00006578302,0.002308395,0.00777715,0.0002417954,0.0001719969,0.0006225898,0.0004512962,0.008008974,0.9588048,0.000558379,0.02081706,0.0001717542],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.4601992,0.00386715,0.5011899,0.001211297,0.0008442609,0.00860539,0.0126329,0.004681372,0.006768499],"genre_scores_gemma":[0.248592,0.003255537,0.7078764,0.0004038132,0.0001508853,0.006332878,0.02667163,0.001141388,0.005575272],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.007065374,"threshold_uncertainty_score":0.03736567,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01270379269268116,"score_gpt":0.2921137774462934,"score_spread":0.2794099847536122,"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."}}