Evaluation of GPU-based Seed Generation for Computational Genomics Using Burrows-Wheeler Transform

@article{Liu2012EvaluationOG,
  title={Evaluation of GPU-based Seed Generation for Computational Genomics Using Burrows-Wheeler Transform},
  author={Yongchao Liu and Bertil Schmidt},
  journal={2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops & PhD Forum},
  year={2012},
  pages={684-690}
}
Unprecedented production of short reads from the new high-throughput sequencers has posed challenges to align short reads to reference genomes with high sensitivity and high speed. Many CPU-based short read aligners have been developed to address this challenge. Among them, one popular approach is the seed-and-extend heuristic. For this heuristic, the first and foremost step is to generate seeds between the input reads and the reference genome, where hash tables are the most frequently used… CONTINUE READING

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