Saturday, August 22, 2015

DNA reverse complement program in Rust

After a very long hiatus, I am starting to write for pleasure again. In addition to posting some opinion pieces here, I am working on another blog, Rusty Bioinformatics, that is more focused on (re)learning bioinformatics programming.

The first post of note is a writing a simple program to provide the reverse complement of a DNA sequence on the command line, written in the Rust programming language. Find it here:

DNA reverse complement in Rust


The AWS genomics ecosystem

This past week, my good friend and collegue at AWS, Chris Crosbie, published a blog post about analyzing whole genome sequence data with one of our genomic analysis platform partners, Seven Bridges Genomics, importing the resulting VCF files to Amazon Redshift, and doing a simple analysis of the data within R and Bioconductor.

The post is lengthy and technically dense, but it is delightful in that it showcases one of the major advantages of working with genomics data on AWS: namely the rich and diverse ecosystem of tools and platform providers that a researcher can bundle together to fit their exact needs.

There has certainly been a failing on my part to communicate the fullness of this ecosystem, and Chris’s post has been a good reminder to me that I need to communicate better (and more often) to the broader bioinformatics community about how to effectively pair down their choices when facing some analysis challenge.

PS: If you like Chris’s post, be sure to read the other one we put together with Matt Wood about uploading dbGaP data to Amazon S3.