The Initiative for the Critical Assessment of Metagenome Interpretation (CAMI)

In just over a decade, metagenomics has developed into a powerful and productive method in microbiology and microbial ecology. The ability to retrieve and organize bits and pieces of genomic DNA from any natural context has opened a window into the vast universe of uncultivated microbes. Tremendous progress has been made in computational approaches to …

Genomic data sharing via BitTorrent, part 2 – BioTorrents to BitTorious

As someone who uses sequence data for most of my research,  I am continually happy with the fact that sequencing continues to get cheaper and easier and faster and bigger and better and more and more and more.  Along with such continued advances, sharing the data produced by such sequencing has become somewhat challenging at …

Comparing the new 16S rRNA V4 and ITS primers to the old primers-RESULTS!

The Knight lab has been working hard testing new primers for 16S rRNA amplicon production and its time to share our progress. So far, the 16S rRNA V4 region forward primer (designated 515f) has been paired with five different reverse primers (806r, 926r, 967r, 1048r, and 1391r) to amplify ribosomal RNA from bacteria, Archaea, and …

Announcing the scikit-bio cookbook “recipe-of-the-week” series

scikit-bio is a library for building bioinformatics tools and workflows in Python. It’s already a core dependency of QIIME, is extensively used in An Introduction to Applied Bioinformatics, and was the subject of my talk at SciPy 2014 (video) this past July. One of our focuses with scikit-bio is to make its functionality very accessible …

Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads (by Rogan Carr and Elhanan Borenstein)

We’d like to first thank Jon for the opportunity to discuss our work in this forum. We recently published a study investigating direct functional annotation of short metagenomic reads that stemmed from protocol development for our lab. Jon invited us to write a blog post on the subject, and we thought it would be a …

New Joint Initiative from the Knight and Sogin Labs as a Follow-up to the MoBEDAC Initiative

If you’ve been reading our posts, you are quite familiar with our efforts at characterizing the bacterial and fungal communities of the built environment. We’ve described our study design, experimental protocols, and results. One thing we may have left you wondering about, however, is the nuts and bolts behind the analyses we and other MoBe …