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.
Apart from gene fusions, Arriba can detect other structural rearrangements with potential clinical relevance, such as exon duplications or truncations of genes (i.e., breakpoints in introns and intergenic regions).
Arriba is the winner of the DREAM SMC-RNA Challenge, an international competition organized by ICGC, TCGA, IBM, and Sage Bionetworks to determine the current gold standard for the detection of gene fusions from RNA-Seq data. The final results of the challenge are posted on the Round 5 Leaderboard.
Apart from the script
draw_fusions.R all software/code of Arriba is disributed under the MIT/Expat License. The script
draw_fusions.R is distributed under the GNU GPL v3 due to dependencies on GPL-licensed R packages. The terms and conditions of both licenses can be found in the LICENSE file.
A dedicated publication about Arriba has not been released yet. Until then, please refer to Arriba in your methods section as follows (or similar):
We used Arriba (https://github.com/suhrig/arriba/) to detect gene fusions from RNA-Seq data.