UdeAlignC: Fast alignment for the compression of DNA reads

Jaime Lotero, Andres Benavides, Anibal Guerra, Sebastian Isaza

Research output: Chapter in Book/InformConference contribution

2 Scopus citations

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.

Original languageEnglish (US)
Title of host publication2018 IEEE Colombian Conference on Communications and Computing, COLCOM 2018 - Proceedings
EditorsDiana Briceno Rodriguez
PublisherInstitute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)9781538668207
DOIs
StatePublished - Sep 14 2018
Externally publishedYes
Event2018 IEEE Colombian Conference on Communications and Computing, COLCOM 2018 - Medellin, Colombia
Duration: May 16 2018May 18 2018

Publication series

Name2018 IEEE Colombian Conference on Communications and Computing, COLCOM 2018 - Proceedings

Conference

Conference2018 IEEE Colombian Conference on Communications and Computing, COLCOM 2018
Country/TerritoryColombia
CityMedellin
Period5/16/185/18/18

All Science Journal Classification (ASJC) codes

  • Computer Networks and Communications
  • Information Systems and Management

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