@inproceedings{a9a2be44a0db46688961a43c5f412380,
title = "UdeAlignC: Fast alignment for the compression of DNA reads",
abstract = "Referential compression algorithms are one of the main strategies to cope with the exponential growth of DNA data available to scientists. One of the techniques used to build a referential compression is sequence alignment, which in turn requires a lot of computing. In this article we present UdeAlignC, a fast alignment algorithm for the compression of DNA reads. We demonstrate that our algorithm is 2× faster than prominent state of the art tools while optimality is only reduced by 5.6\%. We also implement a GPU-accelerated version and show local speedups of up to 12×. Source code available at https://bitbucket.org/BioMRcomp/udealignc.",
author = "Jaime Lotero and Andres Benavides and Anibal Guerra and Sebastian Isaza",
note = "Funding Information: The authors would like to thank the University of Antioquia and Colciencias for funding this research under grants PRV15-2-02 and BEC17-2-27. 978-1-5386-6820-7/18/\$31.00 2018 IEEE Publisher Copyright: {\textcopyright} 2018 IEEE.; 2018 IEEE Colombian Conference on Communications and Computing, COLCOM 2018 ; Conference date: 16-05-2018 Through 18-05-2018",
year = "2018",
month = sep,
day = "14",
doi = "10.1109/ColComCon.2018.8466336",
language = "English (US)",
series = "2018 IEEE Colombian Conference on Communications and Computing, COLCOM 2018 - Proceedings",
publisher = "Institute of Electrical and Electronics Engineers Inc.",
editor = "Rodriguez, \{Diana Briceno\}",
booktitle = "2018 IEEE Colombian Conference on Communications and Computing, COLCOM 2018 - Proceedings",
address = "United States",
}