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Arioc

Arioc

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.

Topic

Sequence analysis; DNA; Nucleic acid structure analysis

Details

  • 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_ jhu.edu
  • Collection: -

Publications

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. https://doi.org/10.1093/bioinformatics/bty167
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 https://doi.org/10.7717/peerj.808
PMID: 25780763
PMCID: PMC4358639


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