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  • Here we introduce CloVR-ITS, an automated pipeline for comparative analysis of internal transcribed spacer (ITS) pyrosequences amplified from metagenomic DNA isolates and representing fungal species. CloVR-ITS is made available as a pre-installed, automated, and portable software pipeline for cloud-friendly execution as part of the CloVR virtual machine package (http://clovr.org). Here we present CloVR-ITS, a standard operating procedure (SOP) for ITS amplicon sequence analysis for fungal diversity studies. CloVR-ITS has been designed to effectively process sequence data representing any contiguous segment of the ITS region (i.e. ITS1 or ITS2) and can perform comparative analysis of hundreds of samples.
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