Cantù Lab @ UC Davis - Annotation Pipeline - EVM based

This Git repository contains the whole pipeline used to generate the structural and functional gene annotation of a grape genome. The pipeline for the assembly of the genome of interest is not included here but is a prerequisite.

Overview

Pipeline

• 0 - External evidences
• 1 - Repeat annotation
• 2 - Training set creation
• 3 - Ab initio predictors training
• 4 - Ab initio prediction
• 5 - Evidence alignment
• 6 - Gene models consensus call (EVM)
• 7 - Filtering
• 8 - Renaming
• 9 - Functional annotation

Requirements

Tools

The following tools are required. Some options and compatibilities might depend on the software version. We successfully ran the pipeline using the versions described below.

• augustus v.3.0.3
• bedtools v.2.26.0
• BLAST v.2.6.0+
• Blast2GO v.4.1.9
• BLAT v.36x2
• busco v.3.0.2
• EVidenceModeler v.1.1.1
• exonerate v.2.2.0
• fastqc v.0.10.1
• genemark v.3.47
• gffcompare v.0.10.1
• gffread
• gmap v.2015-09-29
• hisat2 v.2.0.5
• interproscan v.5.28-67.0
• IsoSeq v.3
• LSC v.2.0
• magicblast v.1.4.0
• maker v.2.31.9
• parallel
• PASA v.2.3.3
• RepeatMasker v.open-4.0.6
• samtools v.1.7
• SNAP v.2006-07-28
• stringtie v.1.3.4d
• TransDecoder v.3.0.1
• trimmomatic v.0.36
• Trinity v.2.6.5

Folder structure

Most of the tools are assumed to be installed in the PATH. If not, the absolute PATH to the Tools directory is given.

2-Annotation
├── 2_0-External_evidences
│   ├── 2_0_1-Proteins
│   └── 2_0_2-mRNAs
│       ├── 2_0_2_1-External_databases
│       ├── 2_0_2_2-RNAseq
│       │   ├── 2_0_2_2_1-RNAseq_reads
│       │   └── 2_0_2_2_2-RNAseq_assembly
│       └── 2_0_2_3-IsoSeq
│           ├── 2_0_2_3_1-IsoSeq_reads
│           └── 2_0_2_3_2-IsoSeq_polishing
├── 2_1-Training
│   ├── 2_1_1-Training_set
│   │   └── pasa_run.log.dir
│   └── 2_1_2-Predictor_training
│       ├── 2_1_2_1-Augustus
│       ├── 2_1_2_2-Genemark
│       └── 2_1_2_3-SNAP
└── 2_2-Prediction
    ├── 2_2_1-Repeats
    ├── 2_2_2-
    ├── 2_2_3-Prediction
    │   ├── 2_2_3_1-BUSCO
    │   ├── 2_2_3_2-Augustus
    │   ├── 2_2_3_3-Genemark
    │   ├── 2_2_3_4-SNAP
    │   └── 2_2_3_5-PASA
    ├── 2_2_4-Transcript_mapping
    ├── 2_2_5-Protein_mapping
    ├── 2_2_6-EVM
    ├── 2_2_7-Annotation_polishing
    ├── 2_2_8-Filtering
    └── 2_2_9-Functional_annotation

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