Predicting bacterial genes using Prokka

I've been predicting genes in bacterial assemblies using Prokka.

The Prokka software has been described in this paper by Seemann (2014).

Prokka predicts protein-coding genes, ribosomal RNA (rRNA) genes, transfer RNA (tRNA) genes, signal leader peptides, and non-coding RNA (ncRNA) genes. Prokka provides an annotation for each predicted gene by finding its best match in large databases such as UniProt and RefSeq and Pfam.

It's very easy to use:

% prokka --outdir myout input.fasta
 

where --outdir points to the directory where you want output to go (e.g. 'myout'),

input.fasta is the input assembly file.

 

The output directory outdir will have a .gff file with the output gene predictions from Prokka.

Yay!