CloVR-16S supports 16S ribosomal RNA sequence analysis to study microbial community compositions. It processes short and long sequence reads from Sanger as well Roche/454 sequencing, including sequence reads generated with the multiplex amplicon 454 pyrosequencing protocol with specifically tagged or barcoded 16S rRNA PCR primers.
The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols:
- QIIME – a Python-based workflow package, allowing for sequence processing and phylogenetic analysis using different methods including the phylogenetic distance metric UniFrac, UCLUST, PyNAST and the RDP Bayesian classifier;
- UCHIME – a tool for rapid identification of chimeric 16S sequence fragments;
- Mothur – a C++-based software package for 16S analysis;
- Metastats and custom R scripts used to generate additional statistical and graphical evaluations.
CloVR-16S accepts as input either a single multiplex sequence dataset (i.e. pooled pyrotagged Roche/454 sequences from multiple combined samples as FASTA and optional QUAL files), or alternatively, multiple separate (pre-processed) sequence files from individual samples.