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 …