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.
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
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- 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
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