arriba¶

Description¶

Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria. It is based on the ultrafast STAR aligner and the post-alignment runtime is typically just ~2 minutes. In contrast to many other fusion detection tools which build on STAR, Arriba does not require to reduce the alignIntronMax parameter of STAR to detect fusions arising from focal deletions.

Environment Modules¶

Run module spider arriba to find out what environment modules are available for this application.

Environment Variables¶

HPC_ARRIBA_DIR - installation directory
HPC_ARRIBA_BIN - executable directory

Citation¶

If you publish research that uses arriba you have to cite it as follows:

[Sebastian Uhrig, Julia Ellermann, Tatjana Walther, Pauline Burkhardt, Martina Fröhlich, Barbara Hutter, Umut H. Toprak, Olaf Neumann, Albrecht Stenzinger, Claudia Scholl, Stefan Fröhling and Benedikt Brors: Accurate and efficient detection of gene fusions from RNA sequencing data. Genome Research. Published in Advance January 13, 2021. https://doi.org/10.1101/gr.257246.119]

Categories¶

phylogenetics