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. Its input can include not only the
alignments of raw reads used by other transcript assemblers, but also
alignments longer sequences that have been assembled from those reads.

In order to identify differentially expressed genes between
experiments, StringTie's output can be processed by specialized
software like Ballgown, Cuffdiff or other programs (DESeq2, edgeR).