ROCker

§ Using existing models

Once you have installed ROCker, the easiest way to use ROCker is by using pre-existing models. We maintain a list of precomputed models that you're free to use.

1. Obtain the model of interest either downloading it from our repository or creating one yourself.
2. Execute ROCker search. The minimum required parameters are:
   $> ROCker search -q input.fasta -k model.rocker -o output.blast
   Where input.fasta is the input metagenome in FastA format, model.rocker is the ROCker model, and output.blast is the output file to be created in tabular BLAST format. For additional supported options, execute:
   $> ROCker search -h
3. If you have a pre-computed BLAST file, you can execute instead:
   $> ROCker filter -x input.blast -k model.rocker -o output.blast
   Where input.blast is the input search to be filtered in tabular BLAST format, model.rocker is the ROCker model, and output.blast is the output file to be created in tabular BLAST format. For additional supported options, execute:
   $> ROCker filter -h

§ Creating models

1. Collect a good reference collection of the gene of interest. You'll need This is the most important step, but there are some resources to help you.