The Velvet Assembler Using OpenACC Directives

10 pages•Published: May 1, 2023

Abstract

There are several programs available in bioinformatics for DNA sequence assembly. This is typically an extremely time-consuming endeavor, as DNA sequences can be extensive and intricate. Velvet was created to combine short and long read sequencing data into larger genomic sequences. Using OpenMP parallel programming, the last version of Velvet was created to support multiple threads. Through OpenACC directives, we present a new version of Velvet that takes advantage of multiprocessing using graphical processing units (GPU). Our tests demonstrate that this extension of Velvet allows for faster performance and efficient memory use.

Keyphrases: bioinformatics, openacc, parallel program, velvet

In: Hisham Al-Mubaid, Tamer Aldwairi and Oliver Eulenstein (editors). Proceedings of International Conference on Bioinformatics and Computational Biology (BICOB-2023), vol 92, pages 72-81.

Links:	https://easychair.org/publications/paper/hq2D
	https://doi.org/10.29007/pzbt

BibTeX entry

@inproceedings{BICOB-2023:Velvet_Assembler_Using_OpenACC,
  author    = {Evaldo Costa and Gabriel Silva},
  title     = {The Velvet Assembler Using OpenACC Directives},
  booktitle = {Proceedings of International Conference on Bioinformatics and Computational Biology (BICOB-2023)},
  editor    = {Hisham Al-Mubaid and Tamer Aldwairi and Oliver Eulenstein},
  series    = {EPiC Series in Computing},
  volume    = {92},
  publisher = {EasyChair},
  bibsource = {EasyChair, https://easychair.org},
  issn      = {2398-7340},
  url       = {/publications/paper/hq2D},
  doi       = {10.29007/pzbt},
  pages     = {72-81},
  year      = {2023}}

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