README.md

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 ftp://ftp.ccb.jhu.edu/pub/data/Arioc, 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(15):2673–2675. 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, 38(8):2081–2087. DOI:10.1093/bioinformatics/btac066

Wilton R, Szalay AS. Short-read aligner performance in germline variant identification. Bioinformatics. 2023, 39(8):1–11. DOI:10.1093/bioinformatics/btad480