Gene Prediction

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. See the Prodigal home page for more info.

To run prodigal on our data, simply type:

cd ~/workdir/assembly/megahit_out

qsub -cwd -N prodigal -l mtc=1 -b y \
/vol/biotools/bin/prodigal -p meta -a final.contigs.genes.faa -d final.contigs.genes.fna -f gff -o final.contigs.genes.gff -i final.contigs.fa

Output files:

final.contigs.genes.gff	positions of predicted genes in GFF format
final.contigs.genes.faa	protein translations of predicted genes
final.contigs.genes.fna	nucleotide sequences of predicted genes