Sunday, February 14, 2016

Methods Matter: Getting Started with the Skin Microbiome

Your choice of sequencing approach matters. Think
about your goals and the methodological caveats
before starting your experiments.
The field of microbiome research has been hugely popular in the past few years. It has forced us to rethink our approaches to various medical practices, and has captured the imaginations of both amateur and professional scientists. With this popularity has come an influx of scientists trying to incorporate the microbiome into their own research. It is of course great that people want to get into the field, but unfortunately it is deceptively difficult for newcomers who are not always aware of how best to get started. This has led to the execution of poorly designed studies that could have been improved by more methodological resources in the literature. To this end, my colleague (and lab mate) led a research project to evaluate the differences between sequencing methods of the skin microbiome, a consideration that is often overlooked by newcomers to the field. This week I want to briefly hit the highlights of the paper and suggest that you read it if you are interested in starting any skin microbiome work.

Sunday, February 7, 2016

The Open Metagenome Toolkit Project

Almost two years ago I started collecting some scripts that I wrote for my own microbial metagenomic analyses. These are some relatively simple Perl and Python scripts that do some common tasks that are required when studying bacterial or viral metagenomes. This collection of scripts if called the Open Metagenome Toolkit. I recently added a few more scripts that I think are helpful, including a script to translate nucleotide sequences and a script to calculate the average lengths of reads. This week our post is about the Open Metagenome Toolkit because it is a cool opportunity for collaborative programming in our microbiome community.