{"id":"W3134848807","doi":"10.1093/plcell/koab077","title":"Long-read sequence assembly: a technical evaluation in barley","year":2021,"lang":"en","type":"article","venue":"The Plant Cell","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":426,"is_retracted":false,"has_abstract":true,"ca_institutions":"Global Institute for Water Security; University of Saskatchewan","funders":"European Regional Development Fund; German Network for Bioinformatics Infrastructure; Canada First Research Excellence Fund; Biotechnology and Biological Sciences Research Council; Grantová Agentura České Republiky; Gatsby Charitable Foundation; Genome Canada","keywords":"Biology; Genome; Triticeae; Hordeum vulgare; Sequence (biology); Sequence assembly; Hybrid genome assembly; Computational biology; Whole genome sequencing; Reference genome; k-mer; Genetics; Gene; Botany; Transcriptome; Poaceae","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00031415,0.0000760179,0.00007612345,0.00001102545,0.00004307926,0.00001194566,0.0001236724,0.00006215639,0.00001938345],"category_scores_gemma":[0.00004823256,0.00005764211,0.00004221113,0.00005850809,0.0000298605,2.888687e-7,0.0001092886,0.00006382531,0.00001189142],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001312018,"about_ca_system_score_gemma":0.0001022418,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002632594,"about_ca_topic_score_gemma":0.0005052392,"domain_scores_codex":[0.9993854,0.00007023317,0.0001091059,0.0001917554,0.0001028187,0.0001407484],"domain_scores_gemma":[0.9996288,0.00002364351,0.00002935805,0.0002463305,0.00005033717,0.00002150762],"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":[0.00001456097,0.00003249895,0.002971215,0.000004847599,0.00001043236,0.000009295603,0.00003761417,0.0002217033,0.9954438,0.00003416662,0.0004283393,0.0007915715],"study_design_scores_gemma":[0.0008185398,0.000129888,0.07470483,0.00002320283,0.00007139557,0.0001341482,0.0001596895,0.0008251501,0.9050431,0.0005570685,0.0172356,0.000297389],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9903821,0.003107979,0.00006458188,0.000255582,0.00008221022,0.0001271037,0.00003177354,0.000001903937,0.005946804],"genre_scores_gemma":[0.998517,0.0006053714,0.0001755055,0.0001712691,0.0000695971,0.00002402668,0.0001011665,0.000006582834,0.0003294335],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.09040065,"threshold_uncertainty_score":0.2350577,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03528134001288496,"score_gpt":0.2687956796789536,"score_spread":0.2335143396660686,"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."}}