Category Archives: paprica
Tutorial: Basic heatmaps and ordination with paprica output
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
Separating bacterial and archaeal reads for analysis with paprica
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
paprica v0.4.0
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
paprica on the cloud
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
Exploring genome content and genomic character with paprica and R
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
Tutorial: Annotating metagenomes with paprica-mg
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