2. Installation

How to install deFusion

deFusion is tested with python 2.7.9.

2.2. Prerequisites:

Under current build, deFusion was designed to identify and ‘defuse’ fused annotated genes in MAKER annotated genomes. Output files generated from a MAKER run are expected to be used as input files for deFusion:

  1. Transcripts in [fasta] format
  2. MAKER genome annotation in [GFF] format
  3. Genome sequence in [fasta] format
  4. MAKER control(ctl) files

2.3. Prepare MAKER control files

MAKER control files maker_bopts.ctl, maker_exe.ctl, maker_opts.ctl provide the basic resource location/path informations for MAKER pipeline. Here we need to create the MAKER controls for the deFusion pipeline, and we only need to change the maker_opts.ctl file.

You can copy those three control files from your previous MAKER run, but with the following changes:

Note: options are set to 0 unless noted in modifications

  • Section: Genome section:

    1. delete genome path
    
  • Section: Re-annotation Using MAKER Derived GFF3:

    2. delete maker_gff path
    3. set rm_pass = 1
    
  • Section: EST Evidence and Protein Homology Evidence:

    4. est=/path/to/your/EST/evidences.fa
    5. protein=/path/to/your/protein/evidences.fa
    
  • Repeat Masking:

    6. set all repeat masking to null or '0'
    7. set softmask=1
    
  • Section: Gene Prediction:

    7. snaphmm=/path/to/SNAP/snap.hmm
    8. augustus_species=augustus_spp
    9. or other gene prediction files
    
  • Section: MAKER Behavior Options:

    10. AED_threshold=1
    11. always_complete=1
    12. keep_preds=1
    

Example MAKER control files: control files

2.4. TODO

Using conda:

conda install --channel bioconda defusion