Monday, May 8, 2017

A Primer on Downloading Sequencing Data from MG-RAST & the SRA

One of the best set of resources we have for bioinformatics, and especially microbiome research, are the extensive and freely available DNA sequence archives. For the past few years, most studies have been (and in most cases required to) archiving their relevant sequence datasets so that they are freely available to the public and other researchers. This is becoming an increasingly valuable resource for data mining and meta-analyses now that we have about a decade of archiving behind us. Just as these  datasets can be highly valuable research tools, they can also be particularly difficult resources to download and prepare for analysis. I have been meaning to get to this for a while, so this week I want to go through an introduction to downloading these datasets. My goal is to equip you to easily get the sequence sets onto your own computer and start your own analysis.