kallisto
Near-optimal RNA-Seq quantification
kallisto is a program for near-optimal quantification of transcript abundances from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the idea of using pseudoalignment to quickly determine reads and targets’ compatibility, with no need for alignment.
According to benchmarks done on a Mac desktop computer, kallisto can quantify 30 million human bulk RNA-seq reads in less than 3 minutes with just the read sequences and a transcriptome...