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https://github.com/animesh/arioc

Arioc: GPU-accelerated DNA short-read alignment

https://github.com/animesh/arioc

Science Score: 13.0%

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    Found 8 DOI reference(s) in README
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Repository

Arioc: GPU-accelerated DNA short-read alignment

Basic Info
  • Host: GitHub
  • Owner: animesh
  • License: bsd-3-clause
  • Default Branch: master
  • Homepage:
  • Size: 13.8 MB
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  • Watchers: 1
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Fork of RWilton/Arioc
Created over 5 years ago · Last pushed over 5 years ago

https://github.com/animesh/Arioc/blob/master/ 

### Arioc:  GPU-accelerated DNA short-read alignment

Download the current release [here](https://github.com/RWilton/Arioc/releases "Arioc releases").

Download the Arioc user guide [here](https://github.com/RWilton/Arioc/blob/master/Arioc.guide.pdf "Arioc user guide") 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](https://tinyurl.com/AriocFTP), the FTP server of the [Center for Computational Biology](http://www.ccb.jhu.edu) at Johns Hopkins University:

| genome | subdirectory | content |
|-|-|-|
| H sapiens | H_sapiens | NCBI GRCh38 patch 12 (WGS, WGBS) |
| M musculus | M_musculus | NCBI GRCm38 patch 6 |
| 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](https://doi.org/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](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty167/4938491?guestAccessKey=72ccdf78-07ee-487c-bf0f-e55da2ed867c)

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](https://doi.org/10.1371/journal.pcbi.1008383)

Owner

  • Name: Ani
  • Login: animesh
  • Kind: user
  • Location: Norway
  • Company: Norwegian University of Science and Technology

A medical graduate from Delhi University with post-graduation in bioinformatics from Jawaharlal Nehru University, India.

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