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Prokka

Annotation tool for bacterial, archaeal, and viral genomes

Prokka uses Prodigal for its ORF predictions.

Download & install Prokka

https://github.com/tseemann/prokka#introduction


Proka requires installation of additional tools: BioPerl, HMMER, etc ..,
apt-get install libdatetime-perl libxml-simple-perl libdigest-md5-perl git default-jre bioperl

# install HMMER
mkdir hmmer
cd hmmer/
wget http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz
tar xvzf hmmer-3.1b1.tar.gz
sudo ./configure && make && make install

see slso:
http://2013-caltech-workshop.readthedocs.org/en/latest/prokka-annotation.html

# download and install prokka
cd $HOME
git clone https://github.com/tseemann/prokka.git
prokka/bin/prokka --setupdb  # prepare sequence database

# add path to your .bashrc file:
export PATH=$PATH:$HOME/prokka/bin

# test
prokka --version
prokka 1.12



Run Prokka

prokka ecoli_genome.fna --outdir Result --prefix ecoli

ls Result/
ecoli.err
ecoli.faa
ecoli.ffn
ecoli.fna
ecoli.fsa
ecoli.gbk
ecoli.gff
ecoli.log
ecoli.sqn
ecoli.tbl
ecoli.txt

Errors

[..] Please rename your contigs or use --centre XXX to generate clean contig names.
Problem: contig names must be shorter than 20 characters to generate valid Genbank files
Solution: (a) Shorten contig names or (b) change variable $MAXCONTIGIDLEN at the top of the bin/prokka script.

Prokka: rapid prokaryotic genome annotation by Torsten Seemann, Bioinformatics, 2014