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 …
The idea for GenomePeek began two years ago when I was working with Karl Klose, Liz Dinsdale, and Rob Edwards to assemble a P. salmonis genome that was being particularly difficult, even though we had 9 gigabases of sequencing. To check whether it was a single isolated genome I pulled out all the 16S reads …
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 …
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 …
Got this in an email from the Bioinformatics Core at the Genome Center. I saw a lot of these mistakes in an NSF Biodiversity panel that I served on earlier this year. One thing I disagree with is the notion that you cannot do bioinformatics on a personal computer. I do this all the time. …
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 …
Posted a request for help on Twitter but I thought it might be of interest to some other people so am also posting about it here. Basically what we (me and Lizzy Wilbanks in my lab) is to take some microbial genomes and to fully annotate all of the repeat elements and all of the …
Metadata collected for MoBE studies can be organized and submitted to QIIME utilizing the MIxS-BE metadata standard. Templates for data submission and a Metadata Standard Submission Guide (see below) will be posted to microbe.net Resources. Please contact Lynn Schriml (lschriml@som.umaryland.edu) for questions regarding mapping your data to the MIxS metadata standard or Gail Ackermann (gail.ackermann@colorado.edu) at QIIME …
Rachel Adams touched on this topic in a post last year, Size matters, or what I learned collaborating with environmental engineers, so I thought I’d revisit it. In her original post, Rachel described that she had been working on methods for air sampling for microbes and when she ran some ideas past her environmental engineering …
A quick post here describing a Gizmodo article highlighting some of the Sloan-funded MBE research presented at the recent AAAS Symposium on Microbiomes of the Built Environment. It talks about work by both Mark Hernandez and Amy Pruden on different aspect of plumbing microbiomes.