<p><strong>Introduction</strong></p>
<p>While metagenomics has been used extensively to study microbial communities from a taxonomic and functional perspective, little has been done to address how the species in a microbiome are adapted to and maintain specific roles in dynamic environments like the rumen.</p>
<p><strong>Rationale</strong></p>
<p>To address this issue we have developed a framework for the robust analysis of metagenomic data that includes fully automated analysis from next-generation sequencing (NGS) reads to assembly, gene predicition and taxonomic identification. Furthermore we imple- ment approaches to estimate SNP diversity in metagenomic samples and carry out statistical tests to identify genes where sequence diver- sity exists.</p
