{"id":"W3215276240","doi":"10.1101/2021.11.22.469599","title":"A metagenomic DNA sequencing assay that is robust against environmental DNA contamination","year":2021,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":4,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Institutes of Health; National Institute of General Medical Sciences; International Development Research Centre; Kenneth Rainin Foundation; Bill and Melinda Gates Foundation","keywords":"Metagenomics; DNA sequencing; Biology; Environmental DNA; DNA extraction; DNA; Contamination; Microbiome; Computational biology; Polymerase chain reaction; Genetics; Gene; Ecology","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.003116044,0.002211228,0.001466663,0.002513318,0.001275428,0.001892253,0.00128915,0.002599904,0.003687497],"category_scores_gemma":[0.006977441,0.001537713,0.00157679,0.001662251,0.001169903,0.001084577,0.002707186,0.002977931,0.00487879],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004389232,"about_ca_system_score_gemma":0.0009923276,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0004472005,"about_ca_topic_score_gemma":0.001615574,"domain_scores_codex":[0.99357,0.001495174,0.0004991642,0.002035499,0.001973042,0.0004272583],"domain_scores_gemma":[0.9966162,0.0009945353,0.0006275926,0.0008295306,0.0005950399,0.0003370389],"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":[0.0001132142,0.00006316146,0.001346611,0.0002329375,0.00008535857,0.00007665509,0.0001147598,0.000344411,0.9877927,0.0006716316,0.001023492,0.008135183],"study_design_scores_gemma":[0.00002964672,0.0002344145,0.003317703,0.00006759055,0.00009739603,0.0004597731,0.0000657565,0.004526867,0.9650816,0.001347161,0.02468844,0.00008358235],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.07101594,0.00164,0.8932505,0.0007001804,0.0006299112,0.001154513,0.01371076,0.01123146,0.006666745],"genre_scores_gemma":[0.124921,0.001866097,0.8376522,0.001217651,0.000248964,0.003556989,0.01710337,0.003401591,0.01003225],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.003687497,"threshold_uncertainty_score":0.01647937,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01703546437177999,"score_gpt":0.2108375996296453,"score_spread":0.1938021352578653,"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."}}