{"id":"W2190884695","doi":"10.1186/s13104-015-1689-4","title":"Choice of reference-guided sequence assembler and SNP caller for analysis of Listeria monocytogenes short-read sequence data greatly influences rates of error","year":2015,"lang":"en","type":"article","venue":"BMC Research Notes","topic":"Listeria monocytogenes in Food Safety","field":"Biochemistry, Genetics and Molecular Biology","cited_by":36,"is_retracted":false,"has_abstract":true,"ca_institutions":"Health Canada","funders":"","keywords":"Reference genome; SNP; Sequence (biology); Computer science; Statistics; k-mer; Biology; Genetics; Mathematics; Single-nucleotide polymorphism; DNA sequencing; Gene; Genotype","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":[0.002140182,0.0002251777,0.0006068865,0.0002869255,0.00006699246,0.00003602448,0.001228735,0.0002338898,0.00001255808],"category_scores_gemma":[0.004187309,0.0001931856,0.0001042895,0.0006640473,0.0008374983,0.00004441302,0.00131948,0.00009686399,4.756604e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003037904,"about_ca_system_score_gemma":0.0006613819,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002388294,"about_ca_topic_score_gemma":0.002098491,"domain_scores_codex":[0.9971611,0.000395092,0.0007349025,0.0007530097,0.0005529607,0.0004029406],"domain_scores_gemma":[0.995752,0.0005890714,0.0002680484,0.001603327,0.001610382,0.0001771266],"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":[0.0004679364,0.00005146888,0.2465743,0.0002313077,0.0004920943,8.810956e-7,0.00008979805,0.0003936279,0.7506835,0.00006502598,0.0001250634,0.0008250601],"study_design_scores_gemma":[0.0006747395,0.0008871835,0.06358767,0.00008506398,0.0003251198,0.000005141401,0.0002764336,0.003951853,0.9278209,0.0001485384,0.001934756,0.0003025467],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9953384,0.001546336,0.00101409,0.00005615792,0.00005198867,0.0004827801,0.001338014,0.000006257663,0.0001659348],"genre_scores_gemma":[0.987457,0.0004008172,0.01098284,0.00001486008,0.00006638073,0.00006259214,0.0009015334,0.00002299662,0.00009094142],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1829866,"threshold_uncertainty_score":0.7877882,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.9184840273526593,"score_gpt":0.6163894904648216,"score_spread":0.3020945368878377,"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."}}