STAMPS course at MBL

A few weeks ago I attended a course entitled “Strategies and Techniques for Analyzing Microbial Population Structure” at the Marine Biological Laboratory in Woods Hole, along with a number of other students, postdocs and faculty engaged in the study of the microbiology of the built environment (as well as the oceans, humans, animals, plants). This excellent …

Sloan Microbiology of the Built Environment Data Analysis Workshop (secrets of QIIME, VAMPS and QIITA)

Submitted to me by Rob Knight. Announcement: Sloan Microbiology of the Built Environment Data Analysis Workshop (secrets of QIIME, VAMPS and QIITA) April 4-5, 2016 University of California, San Diego Application Deadline — February 15, 2016 — mitchellsogin@gmail.com This workshop, staffed by the developers of QIIME, VAMPS and QIITA, invite participants from the Microbiology of …

Issues classifying ITS data? The answer could be simply using “blast” during taxonomy assignment in QIIME

I wrote a post on the Seagrass Microbiome website yesterday about my struggles with fungal ITS sequencing data which I thought I’d share here as well in case anyone is looking to jump into the fungal fray. To summarize: changing the default method of the QIIME assign_taxonomy.py script from “UCLUST” to “blast” dramatically increased the …

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 …

Sloan Microbiology of the Built Environment Data Analysis Workshop (secrets of QIIME, VAMPS and QIITA) January 6-7, 2015

  Announcement: Sloan Microbiology of the Built Environment Data Analysis Workshop (secrets of QIIME, VAMPS and QIITA) January 6-7, 2015 Application Deadline — October 30, 2014 Progress on the microbiology of the built environment, especially through amplicon studies, has been extremely rapid. However, analyzing and combining datasets has been increasingly challenging, especially as investigators use …

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 …

Visualizing millions of DNA sequences – in your web browser!

I’ve been remotely following the Sloan MBE meeting discussions (happening in Boulder, CO this week), and yesterday there was a lot of Twitter discussion focused on data visualization tools. How do we make sense of the millions of DNA sequences we generate from microbial ecology projects in the Built Environment? I thought I’d use this opportunity to highlight …