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Arioc: GPU-accelerated DNA short-read alignment

Download the current release here.

Download the Arioc user guide here or as part of the current release.

Arioc-encoded reference genomes

The Arioc aligners use binary encoded lookup tables as reference genome indexes. For convenience, several Arioc-encoded reference genomes are available for download at, the FTP server of the Center for Computational Biology at Johns Hopkins University:

genome subdirectory content
H sapiens H_sapiens NCBI GRCh38: patch 14 (WGS); patch 13 (WGS, WGBS)
M musculus M_musculus NCBI GRCm39
S cerevisiae S_cerevisiae S288C
T aestivum T_aestivum NCBI GCA_002220425.3 (Triticum 4.0)

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

Wilton R, Szalay AS. Arioc: High-concurrency short-read alignment on multiple GPUs. PLoS Comput Biol. 2020, 16(11):e1008383. DOI:10.1093/10.1371/journal.pcbi.1008383

Wilton R, Szalay AS. Performance optimization in DNA short-read alignment. Bioinformatics. 2022, (in press). DOI:10.1093/bioinformatics/btac066