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, …
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. …
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. …
One of the unmet challenges to the Sloan Foundation’s Microbiology of the Built Environment (MoBE) program is the sharing of the results of the Foundation-funded studies as well as other studies of the indoor and built environment microbiome. At the American Society for Microbiology’s annual conference in Boston last week, I was impressed by Pieter …
Just found an interesting new paper via automated Google Scholar searches: The Bio-Community Perl toolkit for microbial ecology. By Florent Angly, Christopher Fields, and Gene Tyson in Bioinformatics. Here is the abstract: Summary: The development of bioinformatic solutions for microbial ecology in Perl is limited by the lack of modules to represent and manipulate microbial community profiles …
For a summary and list of talks from the QIMME/VAMPS Workshop, see here. Below are the various presentation videos that I recorded at the meeting. Mitch Sogin talks about the capabilities of VAMPS: Rob Knight talks about the capabilities of QIIME: Sue Huse discusses best practices in marker gene analysis (must-see for new …
For those wanting to catch up on the workshop discussions that happened last week in Boulder, we’ve pulled together all the tweets into a Storify! Includes coverage of the QIIME/VAMPS bioinformatics workshop, and the subsequent fungal meeting focused on resources for ITS gene barcoding. [View the story “QIIME/VAMPS and ITS fungi #microbenet meetings” on Storify]
A job of potential interest: Fungi Data Loader & Database Programmer: Browse Jobs. This is in Jason Stajich’s group at UC Riverside (he is working on some aspects of fungi in the built environment, although this job is more general). For more about Jason and his lab see: The Hyphal Tip (his blog) Jason Stajich « Fungal …
Quick post about a meeting that may be of interest to those wanting to learn a bit more about next generation sequencing methods and their uses: Next-Generation Sequencing & Genomic Medicine – Concrete Applications for Research, Drug/Diagnostic Development and Patient Care.
There is an excellent collection of tools and protocols for various microbiome analyses (genomics, metagenomics, rRNA) available at the Human Microbiome Project DACC site. This includes downloadable tools, links to online web servers, and PDFs of various protocols. Definitely worth checking out if you need some tools for sequence analysis.