Team3-Gene Prediction

Team3 Gene Prediction Team:

• Sonali Gupta
  
• Ahish Melkote Sujay
  
• Pallavi Misra
  
• Cheng Shen-Yi
  
• Jie Zhou
  

Summary:

This pipeline is designed to predict genes from assembled genomes using a number of assembly programs and techniques (ab-initio and homology based).

For predicting the coding genes it uses the following programs:

• Prodigal: Ab-initio gene prediction
• GeneMarkS-2: Ab-initio gene prediction
• BLAST: To validate ab-initio coding results
• BEDTools: Tools to merge ab-initio coding results

For predicting the non-coding genes it uses the following programs:

• ARAGORN: a tool for predicting tRNA/tmRNA
• BARRNAP: a tool for predicting rRnNA
• RNAmmer: a tool for predicting rRnNA
• Infernal: a tool for predicting non-coding gene

Pipeline Requirements

Script Execution:

gene_prediction.py -h {Help}
gene_prediction.py -i <Genome Assembly Input Directory> -o <Output Directory> -b <CDS FNA file>

Non-coding only pipeline Execution:

NonCodingPipeline.py -i <path/to/input> -o <path/to/output>

Options

-i dir Directory with fq.gz
-o dir output folder
-b file Reference genome file

Output files:

• gene_prediction.py - Output directory with FASTA files containing coding genes (True positive and False positive in FASTA headers)
  
• NonCodingPipeline.py - Output directory with FASTA files containing no-coding genes