StringTie

StringTie StringTie Transcript assembly and quantification for RNA-Seq CCB » Software » StringTie Home Manual FAQ Overview News Obtaining and installing StringTie Licensing and contact Information Publications Overview 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 alignments of short reads that can also be used by other transcript assemblers, but also alignments of 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, etc.). News 11/13/2025 - v3.0.3 release: addressed cases where --mix with some combination of inputs could cause a crash. prevented -e and --merge usage from including duplicated records for some transcripts in the output GTF.