Subread

Subread is a software tool package for the alignment of both DNA-seq and RNA-seq read data, quantification, and mutation detection. The Subread package consists of five separate tools: 1. Subread, a read aligner for both RNA-seq and DNA-seq data, 2. Subjunc, read aligner for RNA-seq data, detection of exon-exon junctions and gene fusion events, 3. featureCounts, read counting, 4. Sublong, for aligning long reads using the seed-and-vote technique, and 5. exactSNP, a single-nucleotide polymorphism discovery. An R version of the Subread package is also available, Rsubread .