Wrapper#

The wrapper script (ensembl_anno.py) orchestrates the complete annotation workflow.

Basic usage

python ensembl_anno.py \
    --genome_file genome.fa \
    --output_dir output

Analysis groups

  • Repeat annotation

  • Simple feature annotation

  • Transcriptomic annotation

  • Protein annotation

  • Small ncRNA annotation

  • Finalisation

Automatic dependency resolution#

The wrapper enables analyses only when the required inputs are available.

Examples

  • STAR requires short-read FASTQs.

  • minimap2 requires long-read FASTQs.

  • cmsearch requires an Rfam accession file.

  • GenBlast requires protein FASTA.