December Mothur Workshop, part 1

Pat Schloss (pdschloss at gmail.com) offers excellent workshops on the Mothur software for analyzing 16S rRNA data for bacteria. He’s just announced the next one (February 8 to 10, 2016 near the Detroit airport). I had the pleasure of attending the December workshop. A diverse and international group attended the workshop, with many folks who are interested in the human microbiome. …

The Making of MetAnnotate

Blog post prepared jointly by Andrew Doxey (@acdoxey) and Josh Neufeld (@joshdneufeld) The “aquariome” Back in 2013, as part of a project assessing aquarium microbial communities and their role in nutrient cycling, Laura Sauder (graduate student in the Neufeld lab) sequenced a shotgun metagenomic library from a freshwater aquarium biofilter that was installed on this …

Anvi’o: a new platform to work with metagenomic data

Three weeks ago I stood in front of the 60 attendees of the STAMPS course and asked, “How many of you are currently working with shotgun metagenomes?” Ten to fifteen people raised their hands. In contrast, almost all had their hands in the air when I asked how many were expecting to work with shotgun …

CAMI Challenge is Now Open for Participation

Dear metagenome method developers, The first challenge of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI) begins right now! Over the last three months, we received valuable feedback from the community playing with our toy data sets. We incorporated many of your suggestions, thanks again! Today, we proudly release the official data sets …

SciPy 2015 Computational Life and Medical Sciences Mini-Symposium: Call for Abstracts

SciPy 2015 (Scientific Computing with Python) is coming up in Austin, TX this July 6-12. I attended SciPy last year for the first time to present on scikit-bio (see my talk here), and thought it was an excellent meeting. It was great to spend a week talking about software and software development, which isn’t the …

Microbial community, microbiome, and metagenomic analysis tools of the week

Compiling some of the more interesting tools I have seen recently. Some I have plyed with but most I have just looked at the papers briefly. Microbiome | Abstract | VizBin – an application for reference-independent visualization and human-augmented binning of metagenomic data. Global biogeographic sampling of bacterial secondary metabolism GrammR: Graphical Representation and Modeling …

New microbiome tools just keep coming – fun times – hard to keep up

So many new tools and methods in microbiome and microbial community studies and it is just really hard to keep up with them.  Here are some that have caught my eye recently: PLOS ONE: IM-TORNADO: A Tool for Comparison of 16S Reads from Paired-End Libraries. Jeraldo P, Kalari K, Chen X, Bhavsar J, Mangalam A, …

Who are the contaminants in your sequencing project?

Well, been having many discussions recently about PCR amplification happening from “negative” controls where no sample DNA was added. Such amplification is alas pretty common – due to contamination occurring in some other material added to the PCR reaction.  Obviously it would be best to eliminate all DNA contamination of all reagents and all PCRs. …