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

Abstract

The CloVR-Metagenomics pipeline employs several well-known tools and protocols for the analysis of metagenomic whole-genome shotgun (WGS) sequence datasets:A) UCLUST [1] – a C++-based software package for clustering redundant DNA sequences and removing artificial 454 replicates [1];B) BLASTX and BLASTN [2] for functional and taxonomic assignment of sequences, respectively;C) Metastats [3] and custom R scripts to generate additional statistical and graphical evaluation.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.