Among the many tools used for GWAS and Genomic Prediction, there seems to equally as many file formats to navigate. Running multiple different algorithms then requires switching between file formats, which can be a tedious if not time-absorbing task. For both my future sanity as well as yours, I've provided …

In this post, I will be demonstrating how to read FASTQ files using the htsjdk java library and then process those files using functions that allow for parallel processing. I'll be using JShell as described in a previous post, and to begin, we'll designate the class path to the HTSJDK …

I'm a big fan of Java's new read-evaluate-print-loop (REPL) environment, JShell. For beginners in Java, JShell provides a fantastic environment to troubleshoot issues and get comfortable with Java/new packages. As this is a bioinformatics blog, I will be demonstrating how to read FASTA files using the htsjdk (High-throughput sequencing …

In this article I'm going to cover the benefits of using containerized applications. Specifically, I'm going to focus on using Singularity which is the more secure alternative to Docker (which many people have heard of). Not only is Singularity more secure, it was designed with high-performance computing in mind. This …

Time and again I've set up a new Linux environment (for various reasons) and I've found that while there are innumerable ways to go about doing this, I have a few standard steps that I always follow. And the one program to rule them all is: conda !! While most probably …

Throughout my time in bioinformatics, I've found that many people are interested in learning it but don't know how to get started. First, you need to know a few things. You can learn a lot on your own. Just like you can learn a lot about frogs and salamanders without …

I've tried generating static sites on my own before. I've even tried it with pelican and jekyll. And even given all of the great documentation to get started, it still felt a bit overwhelming. So, after yet another attempt to get something that looked like a manageable, visually appealing site …