Category Archives: paprica

The output from our paprica pipeline for microbial community structure analysis and metabolic inference has changed quite a lot over the last few months. In response to some recent requests here’s a tutorial that walks through an ordination and a … Continue reading →

One of the most popular primer sets for 16S rRNA gene amplicon analysis right now is the 515F/806R set. One of the advantages of this pair is that it amplifies broadly across the domains Archaea and Bacteria. This reduces by … Continue reading →

I’m happy to announce the release of paprica v0.4.0.  This release adds a number of new features to our pipeline for evaluating microbial community and metabolic structure.  These include: NCBI taxonomy information for each point of placement on the reference … Continue reading →

This is a quick post to announce that paprica, our pipeline to evaluate community structure and conduct metabolic inference, is now available on the cloud as an Amazon Machine Instance (AMI).  The AMI comes with all dependencies required to execute … Continue reading →

The paprica pipeline was designed to infer the genomic content and genomic characteristics of a set of 16S rRNA gene reads.  To enable this the paprica database organizes this information by phylogeny for many of the completed genomes in Genbank.  … Continue reading →

This tutorial is both a work in progress and a living document.  If you see an error, or want something added, please let me know by leaving a comment. Starting with version 3.0.0 paprica contains a metagenomic annotation module.  This … Continue reading →

This tutorial is both a work in progress and a living document.  If you see an error, or want something added, please let me know by leaving a comment. Building the paprica database provides maximum flexibility but involves more moving … Continue reading →

Last week I gave a talk at the biennial Ocean Sciences Meeting that included some results from analysis with paprica.  Since paprica is a relatively new method I showed the below figure to demonstrate that paprica works.  The figure shows … Continue reading →

This tutorial is both a work in progress and a living document.  If you see an error, or want something added, please let me know by leaving a comment. Getting Started I’ve been making a lot of improvements to paprica, … Continue reading →

The following is a paprica installation tutorial for novice users on Mac OSX (installation on Linux is quite a bit simpler). If you’re comfortable editing your PATH and installing things using bash you probably don’t need to follow this tutorial, … Continue reading →