BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specifi

Ultrafast universal RNA-seq aligner. Aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. STAR has a potential for accurately

Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de

An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with

A package that provides tools for estimating expression in RNA-Seq data which performs sequencing of end tags of transcript, and incorporate molecular