stringtie

Transcript assembly and quantification for RNA-seq

StringTie is a fast and highly efficient assembler of RNA-seq alignments into potential transcripts. The input can be the alignments of raw reads as usual; it also accepts longer assembled sequences. The output can be processed by downstream software including Ballgown, Cuffdiff, etc. Citation: Pertea et al. (2015) StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology 33: 290-295 doi:10.1038/nbt.3122