OTUreporter: Amplicon to report in a single command

While 16S rRNA gene amplicon sequencing is no longer considered a state-of-the-art technique, it is mature and used for the routine screening of samples of microbiological interest. The maturity of the technique and its low costs, have generated a high demand even in areas foreign to typical research.

Here we present a new software tool, OTUreporter. Unlike many automated 16S rRNA gene amplicon tools such those made available by sequencing companies (e.g. Illumina’s "16S Metagenomics" tool), OTUreporter is not a "black box" and uses software that it is actually used in a research context.

OTUreporter uses local data, or can access BaseSpace directly to gather amplicon data and sequencing run details, avoiding any need for the manual download. OTUreporter mainly uses mothur in the background, following a slightly modified version of the standard MiSeqSOP protocol for processing the amplicon data.

The final output of OTUreporter consists on a set of files suitable for downstream analysis (e.g. with phyloseq), as well as a report. This report summarises the details, not only of the analysis, but also of the sequencing jobs themselves. The report, based on a RMarkdown template, creates two different versions of the same: a slimmer printer-friendly pdf document, and an extended html output with interactive content.

OTUreporter analyses are currently available at no additional cost for customers of the Ramaciotti Centre for Genomics.

An additional workflow/analysis mode designed to work with ITS sequences is also integrated within OTUreporter.