Output DescriptionΒΆ

Description of the main outputs:

  • EMACGsingle.sh generates the following output directories:
  1. busco_output_<genome_name>
It contains the output generated by BUSCO (https://busco.ezlab.org/busco_userguide.html#outputs).
  1. FINAL_RESULT

It contains the gff, transcripts and protein prediction files generated by MAKER (http://gmod.org/wiki/MAKER_Tutorial#MAKER.27s_Output).

The hmmsearch results against Pfam database are stored in the subdirectory /annotation_pfam.

Pfam annotated sequences are extracted, and the resulted annotation file (<genome_name>.gff), and sequences (<genome_name>.faa, <genome_name>.fna) are stored in the subdirectory /Genes_with_Pfam_hit.

  1. log_files
log files generated during MAKER predictions are stored here.
  • EMACGpoly.sh generates a directory named Gene_calling_<genome_name> containing the previously described directories.