Hybrid Indexes for Repetitive Datasets

@article{Ferrada2014HybridIF,
  title={Hybrid Indexes for Repetitive Datasets},
  author={Hector Ferrada and Travis Gagie and Tommi Hirvola and Simon J. Puglisi},
  journal={Philosophical transactions. Series A, Mathematical, physical, and engineering sciences},
  year={2014},
  volume={372 2016},
  pages={20130137}
}
Advances in DNA sequencing mean that databases of thousands of human genomes will soon be commonplace. In this paper, we introduce a simple technique for reducing the size of conventional indexes on such highly repetitive texts. Given upper bounds on pattern lengths and edit distances, we pre-process the text with the lossless data compression algorithm LZ77 to obtain a filtered text, for which we store a conventional index. Later, given a query, we find all matches in the filtered text, then… CONTINUE READING
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