Fast and accurate short read alignment with Burrows–Wheeler transform

@inproceedings{Li2009FastAA,
  title={Fast and accurate short read alignment with Burrows–Wheeler transform},
  author={Heng Li and Richard Durbin},
  booktitle={Bioinformatics},
  year={2009}
}
MOTIVATION The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur… CONTINUE READING
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