Team 2, Group 2 - Gene Prediction
This repository contains a pipeline to predict genes from assembled genomes in fasta format.
./genePredictionPipelineT2G2.sh -p /path/to/assemblies
Prodigal, GeneMark-S (or GeneMark-HMM when '-f' flag is used), Rfam, Aragorn, and tRNAscan
1. Put all of the assembled genomes (in fasta format) into a directory
2. Run this command: ./genePredictionPipelineT2G2.sh -p /path/to/assemblies [-f, -h, -t, and -v are optional]
Usage: [-p /path/to/assemblies], [-f to create fasta and gff files], [-g for faster predictions, will run GeneMarkHMM instead of GeneMarkS], [-t to keep temp files and directories], [-v for verbose mode], [-h for help/usage]
input: path to assemblies
temp: results of each individual tool and step (this directory will be removed unless otherwise stated)
output: one gff file per sample containing all predicted genes (union of all 5 tools)
if '-f' is used, fasta files will also be created
For general info, see the project's wiki page.
The repository is organized as follows:
├── final_pipeline.sh # Final gene prediction pipeline
├── README.md # Document you are currently reading, describes the pipeline
├── scripts # Directory containing all of the scripts necessary to run the pipeline
├── results # Directory containing the final results (will be created when pipeline is run)
├── gff # If '-f' is used, results in gff format will be stored here
├── fasta # If '-f' is used, gff to fasta conversion results will be placed here
├── temp # Directory containing temporary files (will be deleted unless '-t' is used)
The temp/ directory is organized as follows (temp directory will be deleted unless '-t' is used):
├── temp/
├── genePrediction
├── prodigalResults # Directory containing results from Prodigal
├── geneMarkResults # Directory containing results from GeneMark-S (or GeneMark-HMM if '-g' is used)
├── rfamResults # Directory containing results from Rfam
├── other # Directory containing files created when Rfam is run
├── aragnoResults # Directory containing results from Aragorn
├──tRNAscanResults # Directory containing results from tRNAscan
├── merging # Directory containing all of the merged results
├── abinitioMerge # Directory containing the merged results of Prodigal and GeneMark
├── ncRNAMerge # Directory containing the merged results of Rfam, Aragorn, and tRNAscan
├── allFiles # Directory containing the merged gff files (before cleaning)
The following tools must be put on the user's PATH env variable, please follow the links for instructions:
GeneMarkS v.4.30: http://opal.biology.gatech.edu/GeneMark/license_download.cgi
Prodigal: https://github.com/hyattpd/Prodigal/blob/GoogleImport/README.md
Infernal: http://eddylab.org/infernal/
tRNAscan-SE: http://lowelab.ucsc.edu/tRNAscan-SE/
Aragorn 1.2.38: http://130.235.46.10/ARAGORN/Downloads/