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ROCker

Accurately detecting functional genes in metagenomes

§ System requirements

  1. Ruby, with the restclient and nokogiri packages. To install required packages execute:
    $> gem install rest_client
    $> gem install nokogiri
  2. R, with the pROC package. To install required packages execute:
    $> R
    R> install.packages('pROC');
  3. A metagenome simulation software: Grinder.
  4. A local search software: NCBI's BLAST+, DIAMOND, or any other software producing a results in the same format of Tabular-BLAST without comments (use the --blast-cmd and --makedb-cmd options to execute any other software).
  5. A multiple alignment software: MUSCLE, or any other software supporting FastA input and output (use the --muscle-cmd option to execute any other software).

§ Installation

Install ROCker using RubyGems:
$> gem install bio-rocker

Or get the source from GitHub:
$> git clone https://github.com/lmrodriguezr/rocker.git

§ License

Artistic license 2.0.

§ Authors

Luis H (Coto) Orellana, Luis M. Rodriguez-R & Konstantinos Konstantinidis, at the Kostas lab.