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Arioc: GPU-accelerated DNA short-read alignment
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README.md

Arioc: GPU-accelerated DNA short-read alignment

The Arioc software is documented in the user guide. Download the user guide directly (click here) or as part of the current release (click here).

Arioc-encoded reference genomes

The reference-genome index structures that Arioc uses are binary-encoded lookup tables. Several interesting Arioc-encoded genomes are will soon be available for download:

genome file content
H sapiens GRCh38.p13.zip NCBI GRCh38 patch 13 (WGS)
H sapiens GRCh38.p13.zip NCBI GRCh38 patch 13 (WGBS)
S cerevisiae S_cerevisiae.zip S288C
T aestivum Triticum_40.zip NCBI GCA_002220425.3

Related publications

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, 3:e808. DOI:10.7717/peerj.808

Wilton R, Li X, Feinberg AP, Szalay AS. Arioc: GPU-accelerated alignment of short bisulfite-treated reads. Bioinformatics. 2018, 34:1-3. DOI:10.1093/bioinformatics/bty167

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