The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon junction detector and featureCounts read summarization program.
NGSEP is an integrated framework for analysis of short and long DNA high throughput sequencing reads. A complete list of functionalities is available in sourceforge (https://sourceforge.net/p/ngsep/wiki/Home/).
BBTools: Official suite of fast, multithreaded bioinformatics tools for DNA/RNA analysis. BBMap aligner, BBDuk trimmer, BBMerge, and 90+ other tools. Actively maintained by Brian Bushnell.