The CloVR-Metagenomics protocol supports the analysis of shotgun sequencing data from total metagenomic DNA sequencing projects. This pipeline utilizes a number of well-known tools for analysis of metagenomic data:

A) UCLUST first clusters redundant sequences that show 99% nucleotide identity and removes artificial 454 replicate reads.

B) Representative DNA sequences are searched against the NCBI COG database using BLASTX.

C) Representative DNA sequences are searched against the NCBI RefSeq database of finished prokaryotic genomes using BLASTN.

E) Metastats and CloVR-implemented R scripts are applied for additional statistical and graphical evaluations of the pipeline results.

CloVR-Metagenomics generates several output reports including taxonomic and functional abundance tables, statistical comparisons of feature abundances between user-defined populations, and heatmaps with unsupervised clusterings of all samples. See SOP for details.
We will sometimes refer to the protocol described above as  CloVR-Metagenomics (no-orfs), which is our default. For users who wish to first call open reading frames (ORFs) on their sequences, we provide an alternative metagenomic analysis protocol that utilizes MetaGene for ORF-calling prior to functional assignment.