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The CloVR-Metagenomics pipeline employs several well-known tools and protocols for the analysis of metagenomic whole-genome shotgun (WGS) sequence datasets:&#xd;&#xa;&#xd;&#xa;A) UCLUST &#x2013; a C++-based software package for clustering redundant DNA sequences and removing artificial 454 replicates;&#xd;&#xa;B) BLASTX and BLASTN for functional and taxonomic assignment of sequences, respectively;&#xd;&#xa;C) Metastats and custom R scripts to generate additional statistical and graphical evaluation.&#xd;&#xa;&#xd;&#xa;The CloVR-Metagenomics pipeline accepts as input multiple fasta files (1 sample per file) and a corresponding tab-delimited metadata file that specifies features associated with the samples, which are used for comparative analysis. This protocol is available in CloVR beta version 0.5 and 0.6

nature precedings

CloVR-Metagenomics: Functional and taxonomic microbial community characterization from metagenomic whole-genome shotgun (WGS) sequences – standard operating procedure, version 1.0