To provide users with an option to analyze metagenomic data with predicting specific peptide fragments, here we describe an alternative CloVR-Metagenomics track (orfs) that utilizes a different functional characterization protocol:
A) UCLUST first clusters redundant reads that show 99% nucleotide identity and removes any artificial 454 replicate sequences.
B) MetaGene predicts protein-coding genes on partial gene fragments.
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.
Executing this pipeline is identical to the original CloVR-Metagenomics walkthrough — simply substitute the following config file: