StringTie 2016

Introduction

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. ¹

Installed version

The currently installed version is available on environment hpc-env/6.4:

StringTie/1.3.5-GCCcore-6.4.0

Using StringTie

If you want to find out more about StringTie on the HPC Cluster, you can use the command

module spider StringTie

This will show you basic informations e.g. a short description and the currently installed version.

To load the desired version of the module, use the command, e.g.

module load StringTie

Always remember: this command is case sensitive!

A short overview about the usage of StringTie can be listed with the help function:

stringtie --help

Documentation

A short summary about the program and the version history can be found here
The program's manual can be found here.