{"id":"W2112491476","doi":"10.1093/bioinformatics/btp367","title":"<i>De novo</i> transcriptome assembly with ABySS","year":2009,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Gene expression and cancer classification","field":"Biochemistry, Genetics and Molecular Biology","cited_by":410,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Cancer Agency","funders":"Genome British Columbia; Michael Smith Health Research BC; National Cancer Institute; Genome Canada","keywords":"Contig; Sequence assembly; Transcriptome; Genome; Computational biology; Java; Biology; De novo transcriptome assembly; Software; Computer science; Hybrid genome assembly; Source code; Shotgun sequencing; Reference genome; Perl; Genetics; Gene; Programming language; Gene expression","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":[0.001255243,0.00135697,0.001077289,0.001365208,0.001240932,0.001417599,0.001341532,0.000473187,0.01085775],"category_scores_gemma":[0.002508519,0.0007159594,0.0009406978,0.001998946,0.0003408731,0.0009607808,0.001017283,0.001632274,0.01074004],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006508848,"about_ca_system_score_gemma":0.001148939,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002905208,"about_ca_topic_score_gemma":0.002795181,"domain_scores_codex":[0.9993291,0.00009023656,0.00007970218,0.0002475982,0.00018667,0.00006675911],"domain_scores_gemma":[0.9990481,0.0002372529,0.0001380167,0.0002157884,0.0002767429,0.00008413003],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.001874581,0.0003061548,0.009438693,0.00243257,0.0002616401,0.0007770505,0.001042124,0.01291445,0.6658593,0.007731067,0.1010009,0.1963614],"study_design_scores_gemma":[0.0002451697,0.0003221306,0.01809814,0.0002120205,0.0001896128,0.001120157,0.000238528,0.118048,0.6131237,0.0142615,0.2339628,0.0001782109],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.07456221,0.000832986,0.7816455,0.0007854522,0.0004173405,0.0006638335,0.05449798,0.07887584,0.007718813],"genre_scores_gemma":[0.05934261,0.0006425941,0.8372577,0.0002591162,0.0001018689,0.001048399,0.08777719,0.008014159,0.00555637],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.01085775,"threshold_uncertainty_score":0.03632283,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009809137250629119,"score_gpt":0.2413464444821044,"score_spread":0.2315373072314753,"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."}}