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

Detail

  • Operation: Read mapping;Mapping assembly;DNA mapping

  • Software interface: Command-line user interface

  • Language: C++

  • License: BSD-3-Clause

  • Cost: Free

  • Version name: 1.41

  • Credit: The National Institutes of Health

  • Input: -

  • Output: -

  • Contact: richard.wilton@jhu.edu

  • Collection: -

  • Maturity: -

Publications

  • Arioc: GPU-accelerated alignment of short bisulfite-treated reads.
  • Wilton R, et al. Arioc: GPU-accelerated alignment of short bisulfite-treated reads. Arioc: GPU-accelerated alignment of short bisulfite-treated reads. 2018; 34:2673-2675. doi: 10.1093/bioinformatics/bty167
  • https://doi.org/10.1093/bioinformatics/bty167
  • PMID: 29554207
  • PMC: PMC6061805
  • Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space.
  • Wilton R, Budavari T, Langmead B, Wheelan SJ, Salzberg SL, et al. (2015). Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space. PeerJ 3: e808.
  • https://doi.org/10.7717/peerj.808
  • PMID: 25780763
  • PMC: PMC4358639

Download and documentation

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