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. Get deFusion

Download deFusion from GitHub:

git clone https://github.com/wjidea/defusion

2.5. TODO

Using conda:

conda install --channel bioconda defusion