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.).

Version: 2.1.6(G100) 1.3.1 (Marconi)

Availability: GALILEO100, MARCONI

Target: all

Official web site:

Related Commands:

$ module load profile/bioinf

$ module load autoload stringtie

$ stringtie [options]

More informations are showed typing:

$ stringtie -h

Help and Documentation:

You can find documentation on the system, with the command 'module help stringtie

- The manual is on the web at the original home page (


CINECA consultants can be reached through the address:'''

contact =