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
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
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
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