{"id":"W4400597743","doi":"10.1093/bioinformatics/btae448","title":"isolateR: an R package for generating microbial libraries from Sanger sequencing data","year":2024,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Saskatchewan; University of Guelph","funders":"Breakthrough T1D Canada; Canada First Research Excellence Fund; National Institute of General Medical Sciences; Canada Research Chairs","keywords":"Cataloging; Sanger sequencing; Benchmarking; Computer science; Biology; Pipeline (software); Computational biology; Information retrieval; DNA sequencing; World Wide Web; Genetics; Programming language; Gene","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":[0.007494866,0.005535456,0.004401592,0.003418276,0.001121037,0.0044773,0.004940022,0.001713245,0.0678027],"category_scores_gemma":[0.02520575,0.00300609,0.003502814,0.002804139,0.001455479,0.002913367,0.004481889,0.005333986,0.09098987],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009810681,"about_ca_system_score_gemma":0.003838842,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002092036,"about_ca_topic_score_gemma":0.002448395,"domain_scores_codex":[0.9958723,0.001699303,0.0003587036,0.0009160769,0.0008232585,0.0003304013],"domain_scores_gemma":[0.9920295,0.004789114,0.000965533,0.001079528,0.0007356415,0.000400548],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.001859298,0.00017283,0.004775735,0.009651328,0.002109873,0.0009484572,0.0008658186,0.01245349,0.0197201,0.01913083,0.8212236,0.1070888],"study_design_scores_gemma":[0.001662396,0.0004055817,0.005035574,0.001606813,0.0009441566,0.001340419,0.0002318268,0.06663733,0.02713413,0.05020273,0.8442749,0.0005240709],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.002764809,0.001278025,0.3434949,0.0006440642,0.0003818446,0.0005989288,0.102967,0.5417494,0.006121003],"genre_scores_gemma":[0.02524008,0.002004332,0.5752556,0.001435963,0.0002119782,0.004374477,0.1604408,0.2237896,0.007247198],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.0678027,"threshold_uncertainty_score":0.2268226,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04105578436180538,"score_gpt":0.2622596653762032,"score_spread":0.2212038810143978,"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."}}