CloVR-Metagenomics (orfs) version 1.0

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.

D) Predicted peptide fragments with more than 90% amino acid identity are clustered and representatives from each cluster compared against the NCBI COG database using BLASTP.

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:

File: CloVR-Metagenomics (orfs) config file

CloVR Metagenomics workflow