MAKER2 Pipeline

For Snakemake implementation of the MAKER2 pipeline, see MAKER2-snakemake

1. Installation

1.1 Install Dependencies

• RepeatModeler
• RepeatMasker
• MAKER2
• GenemarkES
• Augustus
• SNAP
• BUSCO

1.2 Install Databases

• wget https://www.dfam.org/releases/Dfam_3.2/families/Dfam.h5.gz

1.2 Install myMAKER2-Pipeline

• Download from GitHub:

2. Usage

2.1 Data

• Place genome, est data, and protein homology data in data/ directory
  • Name genome as **orgname**.genome.fas
  • Name est data as **orgname**.est.fas
  • Name protein homology data as **orgname**.protein.fas
• Where **orgname** is the name of the organism. This will be different if est and protein data originates from alternate organism
• See example/data/ to see where and how data files should be placed and named.

2.2 Command Line

• python3 maker_run.py [options]
  • -p PASSAGE, --passage PASSAGE : Passage number through MAKER2 pipeline (i.e. 1, 2, 3, or 4), default:1
  • -t THREADS, --threads THREADS : Number of threads, default:1
  • -a, --alt_est : If est and protein homology data come from an alternate organims, default:False

2.3 MAKER2 ctl

• All Passes

  • genome = path to genome
  • rm_lib = path to RepeatModeler output
  • protein = path to protein homology data (can be from closely related organism)
  • est = path to est data from same organism (blank if from alternate organism)
  • altest = path to est data from alternate organism (blank if from same organism)

• Passes 2, 3, & 4

  • snaphmm = path to SNAP hmm
  • gmhmm = path to GeneMark hmm
  • augustus_species = name of AUGUSTUS species (species model produced by BUSCO)
  • maker_gff = path to MAKER2 derived gff

• Pass 1 (only evidence based gene models are reported)

  • est2genome = 1
  • protein2genome = 1
  • keep_preps = 0

• Passes 2 & 3 (only gene models supported by homology evidence are reported)

  • est2genome = 0
  • protein2genome = 0
  • keep_preps = 0

• Pass 4 (all gene models are reported)

  • est2genome = 0
  • protein2genome = 0
  • keep_preps = 1

*SNAP and Augustus are retrained between passes
*GeneMarkES is self trained

References