Sunday, August 24, 2014

A Microbiome Analysis Toolkit and "Block Fasta" Formatting

I write a lot of scripts in my day-to-day sequence analysis of microbiome data.  While a lot of these are a bit project specific, some of these could be useful for others in their sequence analysis projects.  A while back I posted about a script for formatting Qiime output files for input into the Lefse analysis toolkit, but now I am thinking it would be worth adding more.  Therefore, I changed the "Lefse formatting" repository to be a more general "microbiome sequence analysis toolkit" repository.  This seems like a nice place to periodically add scripts for easy use by others.  To get this new repo started, I added a new script for removing "block fasta" formatting from fasta sequence files.  It's relatively simple, but I think it's also pretty useful.

Sunday, August 3, 2014

To Create an Online Forum for the Virus Ecology Research Community

 The Marine Microbiology Initiative is striving to build a
community of virus ecology resources online.
Like bacteria and fungus ecology, virus ecology is an important part of the functioning world around us, as well as an important aspect of our health and wellbeing (viruses are part of the human microbiome after all).  While there is a lot of great virus ecology research going on, there remains a lack of communication and standardization throughout the field.  For example, there are a lot of great analytical tools available online, but it is often unclear which is the best suited for certain analyses, especially for those entering the field.  This lack of communication and research is hindering the research potential of the field as it moves forward.  Luckily for us, the awesome people at the Gordon and Betty Moore Foundation Marine Microbiology Initiative are working on implementing online tools for enhancing communication and methodological standardization across the field.  In this post, I just want to spread the word about their project and their call for proposals.