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How does fusion gene detection thru RNA-seq compare to FDA approved kits? ymc RNA Sequencing 0 09-11-2013 05:59 PM

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Old 02-15-2018, 11:53 AM   #1
uhrigs
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Location: Heidelberg

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Default Arriba: Fast and accurate gene fusion detection from RNA-Seq data

Dear all,

We developed an algorithm called "Arriba" to detect gene fusions from RNA-Seq data of tumor samples. It is based on the ultrafast STAR aligner (https://github.com/alexdobin/STAR) 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.

But Arriba is not only fast, it is also very accurate: It is currently the best-performing algorithm in the ongoing ICGC-TCGA DREAM SMC Challenge about gene fusion algorithms (final results pending):
https://www.synapse.org/#!Synapse:sy...89/wiki/423306

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/

Best regards,
Sebastian
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Old 02-21-2018, 01:56 AM   #2
pli
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Hi Sebastian,

has, or will this method be published? Would be nice. Cheers,

P
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Old 02-21-2018, 01:37 PM   #3
uhrigs
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Yes, the method will certainly be published. I have just started working on the manuscript. Stay tuned ...
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cancer, fusion, rna-seq, variant calling

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