Accurately detecting functional genes in metagenomes.
-
Ruby, with the restclient and nokogiri packages. To install the required packages execute:
$> gem install rest-client $> gem install nokogiri $> gem install json
-
R, with the pROC package. To install the required packages, execute:
$> R R> install.packages('pROC');
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A metagenome simulation software: Grinder.
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A local search software: NCBI BLAST+, DIAMOND, or any other software producing a results in the same format of Tabular-BLAST without comments (use the
--search-cmd
and--makedb-cmd
options to execute any other software). -
A multiple alignment software: MUSCLE, Clustal Omega or any other software supporting FastA input and output (use the
--aligner-cmd
option to execute any other software).
Install ROCker using RubyGems:
$> gem install bio-rocker
Or get the source from GitHub:
$> git clone https://github.com/lmrodriguezr/rocker.git
$> ./rocker/bin/rocker
Luis H (Coto) Orellana, Luis M. Rodriguez-R & Konstantinos Konstantinidis, at the Kostas lab.