Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data of tumor samples. It is based on the ultrafast STAR aligner and the post-alignment runtime is typically just ~2 minutes. Hence, fusion detection comes at virtually no cost, since the alignment of FastQ reads is a task that needs to be done anyway in a typical RNA-Seq workflow.
Arriba has been submitted to 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. As of round 4, Arriba is the best-performing algorithm.
Some more highlights:
- ability to detect intergenic and intronic breakpoints
- ability to detect exon duplications/inversions
- utilization of structural variants obtained from whole-genome sequencing
- filtering of transcript variants observed in healthy tissue
- comprehensive manual available at http://arriba.readthedocs.io/
- simple installation routine; especially, if you already use STAR
We would be glad, if you could give it a try, and are happy to receive feedback! Please visit the homepage to download the code or in case you need help: https://github.com/suhrig/arriba/