During the Introduction to Metagenomics Summer Workshop we discussed denoising amplicon sequence variants and worked through Ben Callahan’s DADA2 tutorial. During that session, I mentioned several other approaches and algorithms for denoising or clustering amplicon sequence data including UNOISE3, DeBlur and Mothur. I also mentioned I would try to post some example workflows for some of these other approaches to highlight the similarities, as well as the differences. It looks like I am just now getting around to it.
A collaborator recently asked if I could help pull down a few thousand sequence files from the NCBI Sequence Read Archive (SRA) for a secondary analysis. This is a short post primarily to help me (and hopefully others) remember how to do this once you have a set of SRR IDs of interest.
While I came across several great resources providing information on how to download SRA files using the SRA Toolkit, I wanted to retain just the basics, and some example code, should this type of request come across my desk again in the future.