Rsubread
Rsubread is a software package written in R that provides fast and accurate alignment of high‑throughput sequencing reads to reference genomes and efficient summarization of read counts for downstream analysis. It includes the command line utilities align, subjunc and featureCounts, as well as an R interface that allows users to perform alignment, splicing junction detection, and feature counting within a single R script. The package was developed by the Computational Genomics Group at the Genome Institute of Singapore and released under an open‑source license.
The aligner uses a seed‑based approach that builds a Burrows‑Wheeler transform of the reference sequence, followed
Rsubread is designed to be lightweight and easy to install from CRAN or Bioconductor. It supports a
Benchmarks comparing Rsubread to other aligners such as STAR and TopHat2 show comparable or superior accuracy