CRAM is a tool developed to analyze data produced from shotgun metagenome sequencing. CRAM was created for people who are familiar with UNIX and command-line interfaces and enables scientists to modify their analysis approach to fit their experiment. It was created to provide an alternative to one-size-fits-all approaches to metagenome annotation.
The default pipeline consists of an assemble, annotate and quantify approach to metagenome analysis. The creation of quantitative data allows for comparison between samples across other variables such as time and space. If this does not suit you, you can easily craft your own approach.
Oh yeah, CRAM and the tools that it is built from are 100% free and open source because science with black boxes is not science.
To learn how to install and use CRAM, visit the wiki.
BSD (see LICENSE.txt)