Index

A

augustus_output_to_gtf() (in module ensembl.tools.anno.transcriptomic_annotation.augustus)

C

create_slice_hints_file() (in module ensembl.tools.anno.transcriptomic_annotation.augustus)

E

ensembl.tools.anno.protein_annotation.genblast module ensembl.tools.anno.protein_annotation.miniprot module ensembl.tools.anno.repeat_annotation.dust module ensembl.tools.anno.repeat_annotation.red module ensembl.tools.anno.repeat_annotation.repeatmasker module ensembl.tools.anno.repeat_annotation.trf module ensembl.tools.anno.simple_feature_annotation.cpg module ensembl.tools.anno.simple_feature_annotation.eponine module

ensembl.tools.anno.snc_rna_annotation.cmsearch module ensembl.tools.anno.snc_rna_annotation.trnascan module ensembl.tools.anno.transcriptomic_annotation.augustus module ensembl.tools.anno.transcriptomic_annotation.minimap module ensembl.tools.anno.transcriptomic_annotation.scallop module ensembl.tools.anno.transcriptomic_annotation.star module ensembl.tools.anno.transcriptomic_annotation.stringtie module

G

generate_hints() (in module ensembl.tools.anno.transcriptomic_annotation.augustus)

M

module ensembl.tools.anno.protein_annotation.genblast ensembl.tools.anno.protein_annotation.miniprot ensembl.tools.anno.repeat_annotation.dust ensembl.tools.anno.repeat_annotation.red ensembl.tools.anno.repeat_annotation.repeatmasker ensembl.tools.anno.repeat_annotation.trf ensembl.tools.anno.simple_feature_annotation.cpg ensembl.tools.anno.simple_feature_annotation.eponine ensembl.tools.anno.snc_rna_annotation.cmsearch ensembl.tools.anno.snc_rna_annotation.trnascan ensembl.tools.anno.transcriptomic_annotation.augustus ensembl.tools.anno.transcriptomic_annotation.minimap ensembl.tools.anno.transcriptomic_annotation.scallop ensembl.tools.anno.transcriptomic_annotation.star ensembl.tools.anno.transcriptomic_annotation.stringtie

multiprocess_augustus_hints() (in module ensembl.tools.anno.transcriptomic_annotation.augustus) multiprocess_augustus_id() (in module ensembl.tools.anno.transcriptomic_annotation.augustus)

R

run_augustus_predict() (in module ensembl.tools.anno.transcriptomic_annotation.augustus) run_cmsearch() (in module ensembl.tools.anno.snc_rna_annotation.cmsearch) run_cpg() (in module ensembl.tools.anno.simple_feature_annotation.cpg) run_dust() (in module ensembl.tools.anno.repeat_annotation.dust) run_eponine() (in module ensembl.tools.anno.simple_feature_annotation.eponine) run_genblast() (in module ensembl.tools.anno.protein_annotation.genblast) run_minimap2() (in module ensembl.tools.anno.transcriptomic_annotation.minimap) run_miniprot() (in module ensembl.tools.anno.protein_annotation.miniprot)

run_red() (in module ensembl.tools.anno.repeat_annotation.red) run_repeatmasker() (in module ensembl.tools.anno.repeat_annotation.repeatmasker) run_scallop() (in module ensembl.tools.anno.transcriptomic_annotation.scallop) run_star() (in module ensembl.tools.anno.transcriptomic_annotation.star) run_stringtie() (in module ensembl.tools.anno.transcriptomic_annotation.stringtie) run_trf() (in module ensembl.tools.anno.repeat_annotation.trf) run_trimming() (in module ensembl.tools.anno.transcriptomic_annotation.star) run_trnascan() (in module ensembl.tools.anno.snc_rna_annotation.trnascan)

S

subsample_transcriptomic_data() (in module ensembl.tools.anno.transcriptomic_annotation.star)