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 .., # install HMMERapt-get install libdatetime-perl libxml-simple-perl libdigest-md5-perl git default-jre bioperl 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: # download and install prokka
# add path to your .bashrc file:cd $HOME git clone https://github.com/tseemann/prokka.git
prokka/bin/prokka --setupdb # prepare sequence databaseexport PATH=$PATH:$HOME/prokka/bin # test prokka --version prokka 1.12 ls Result/ ecoli.err ecoli.faa ecoli.ffn ecoli.fna ecoli.fsa ecoli.gbk ecoli.gff ecoli.log ecoli.sqn ecoli.tbl ecoli.txt 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.
|