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.
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.