StringTie is a 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 novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.
The Center for Computational Biology at Johns Hopkins University
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Nat Biotechnol. 2015 Mar;33(3):290-5. doi: 10.1038/nbt.3122. Epub 2015 Feb 18.
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.
Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL