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Arioc is a set of tools to align short bisulfite-treated DNA sequences (BS-seq reads) to long reference DNA sequences. The Arioc algorithm runs both in GPU and CPU and uses parallel sort and reduction routines to distinguish locations of likely alignments.


Sequence analysis; DNA; Nucleic acid structure analysis


  • Operation: Read mapping; Mapping assembly; DNA mapping
  • Software interface: Command-line user interface
  • Language: C++
  • Operating system: Linux; Microsoft Windows
  • License: BSD-3-Clause
  • Cost: Free
  • Version name: 1.41
  • Credit: The National Institutes of Health
  • Contact: richard.wilton _at_
  • Collection: -


Wilton R, Li X, Feinberg AP, Szalay AS "Arioc: GPU-accelerated alignment of short bisulfite-treated reads." Bioinformatics. 2018 Aug 1;34(15):2673-2675.
PMID: 29554207
PMCID: PMC6061805

Wilton R, Budavari T, Langmead B, Wheelan SJ, Salzberg SL, Szalay AS "Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space." PeerJ, 2015
PMID: 25780763
PMCID: PMC4358639

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