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