{"id":"W4408908307","doi":"10.1002/cpz1.70124","title":"Streaming Long‐Read Sequence Alignments for HLA Predictions Using HLAminer","year":2025,"lang":"en","type":"article","venue":"Current Protocols","topic":"T-cell and B-cell Immunology","field":"Immunology and Microbiology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; Genome British Columbia","funders":"Canadian Institutes of Health Research","keywords":"Computer science; Nanopore sequencing; Human leukocyte antigen; Protocol (science); Software; DNA sequencing; MIT License; Shotgun sequencing; Source code; Hybrid genome assembly; Computational biology; Data mining; Biology; Genetics; Gene; Programming language","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":[0.002525343,0.001550385,0.0008643957,0.0009511199,0.0008831671,0.001214286,0.00202573,0.001199251,0.01487256],"category_scores_gemma":[0.006388811,0.001361589,0.001001438,0.0009171522,0.0003971298,0.00156511,0.0014302,0.003012068,0.0141736],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007668677,"about_ca_system_score_gemma":0.00146056,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001979413,"about_ca_topic_score_gemma":0.004494728,"domain_scores_codex":[0.9986482,0.0002394341,0.0001821349,0.000467662,0.0003864846,0.00007612021],"domain_scores_gemma":[0.9985942,0.0006158367,0.0001429487,0.0002603666,0.0003073575,0.00007927407],"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":[0.002332559,0.0003266245,0.006181046,0.002266164,0.0004352621,0.000590281,0.0007787393,0.01697624,0.5480039,0.01195646,0.1720094,0.2381434],"study_design_scores_gemma":[0.0003282336,0.0003122415,0.004709702,0.0002108125,0.0001045639,0.0005117312,0.0001325811,0.2797362,0.5517197,0.01435351,0.1475922,0.0002885733],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"protocol","genre_scores_codex":[0.03237717,0.0009847943,0.7529709,0.0006492541,0.0003682214,0.000766351,0.03412652,0.1720657,0.005691052],"genre_scores_gemma":[0.05213613,0.0004264656,0.8979415,0.000550654,0.00005822623,0.001925709,0.03236175,0.009818948,0.004780711],"genre_candidate":"protocol","genre_consensus":null,"teacher_disagreement_score":0.01487256,"threshold_uncertainty_score":0.04975367,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.07443846455481846,"score_gpt":0.3725897048677749,"score_spread":0.2981512403129564,"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."}}