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.
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White, J., Arze, C., Matalka, M. et al. CloVR-Metagenomics: Functional and taxonomic microbial community characterization from metagenomic whole-genome shotgun (WGS) sequences – standard operating procedure, version 1.0. Nat Prec (2011). https://doi.org/10.1038/npre.2011.5886.1
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DOI: https://doi.org/10.1038/npre.2011.5886.1