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

https://github.com/tseemann/prokka#invoking-prokka

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.

see https://github.com/tseemann/prokka/issues/118

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