{"id":"W3151743941","doi":"10.1093/bib/bbab102","title":"Choice of assemblers has a critical impact on de novo assembly of SARS-CoV-2 genome and characterizing variants","year":2021,"lang":"en","type":"article","venue":"Briefings in Bioinformatics","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":67,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"","keywords":"Sequence assembly; Contig; Genome; Metagenomics; Biology; Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); Coronavirus disease 2019 (COVID-19); Computational biology; Coronavirus; DNA sequencing; Pandemic; 2019-20 coronavirus outbreak; Genetics; Virus; Gene; Virology; Infectious disease (medical specialty); Disease; Medicine; Transcriptome","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005840897,0.0002019961,0.0005720155,0.0003059446,0.0000515232,0.00007330332,0.0001430247,0.0001842672,0.000005127642],"category_scores_gemma":[0.002147512,0.0001818582,0.0001186774,0.000493695,0.0001976042,0.0002705732,0.000129358,0.0003569586,0.000008483281],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001550912,"about_ca_system_score_gemma":0.0007725638,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003817632,"about_ca_topic_score_gemma":0.00001786508,"domain_scores_codex":[0.998098,0.00004458745,0.0007133489,0.0001782291,0.0004771597,0.0004886499],"domain_scores_gemma":[0.9986184,0.0005537758,0.0001658011,0.0003523471,0.0002509026,0.00005872474],"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":[0.0002627649,0.0003311742,0.02166513,0.001658998,0.00009709521,0.0001376226,0.002216938,9.82505e-7,0.9708787,0.000461434,0.0001063317,0.002182854],"study_design_scores_gemma":[0.002911562,0.0007077996,0.2245124,0.001188069,0.00008119321,0.0005137689,0.000360793,0.01144753,0.7539858,0.0001495737,0.003840339,0.0003012056],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9954553,0.0001252079,0.0006365295,0.001190173,0.00003795508,0.0002023023,0.00003151047,0.0000209205,0.002300119],"genre_scores_gemma":[0.9716219,0.0000214203,0.004111409,0.02416264,0.00004039942,0.000007322696,0.000007646029,0.00002379185,0.00000348332],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2168929,"threshold_uncertainty_score":0.7415962,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.08552310205741168,"score_gpt":0.3863838174477084,"score_spread":0.3008607153902967,"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."}}