{"id":"W2903125175","doi":"10.1186/s12859-018-2485-7","title":"Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies","year":2018,"lang":"en","type":"article","venue":"BMC Bioinformatics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1285,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Wine Australia; Australian Government; Alberta Water Research Institute; Bioplatforms Australia","keywords":"Contig; Genome; Ploidy; Biology; Haplotype; Genetics; Sequence assembly; Purge; Computational biology; Allele; Gene; Transcriptome","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.003932375,0.002122416,0.001402985,0.002128466,0.001480866,0.002335866,0.00193932,0.001181508,0.01071021],"category_scores_gemma":[0.006816694,0.001974668,0.002094789,0.001391844,0.0007924602,0.001550886,0.003081233,0.002860344,0.006654101],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001017942,"about_ca_system_score_gemma":0.001580959,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00263769,"about_ca_topic_score_gemma":0.004696571,"domain_scores_codex":[0.9982916,0.0002599627,0.0001674025,0.0006704593,0.0004734338,0.0001371385],"domain_scores_gemma":[0.9971122,0.001101715,0.0004324789,0.0007414519,0.0004223151,0.0001899309],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.003218203,0.0003147244,0.01878117,0.00411464,0.0009795267,0.002133916,0.003377171,0.0242225,0.4352126,0.008585918,0.08436553,0.4146941],"study_design_scores_gemma":[0.0005040031,0.0006452704,0.02011411,0.0004288079,0.0004266484,0.002463349,0.0004991647,0.1355445,0.5295796,0.008767663,0.3005149,0.0005119283],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.06524167,0.001310703,0.7492672,0.0003213305,0.0004848719,0.0009372025,0.01435561,0.163041,0.005040406],"genre_scores_gemma":[0.09269521,0.0004998283,0.8423929,0.0003395935,0.00006524081,0.0008923107,0.04014789,0.01859182,0.004375278],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01071021,"threshold_uncertainty_score":0.03582925,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02474087615458948,"score_gpt":0.2563884776234654,"score_spread":0.2316476014688759,"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."}}