AmpliVar: mutation detection in high-throughput sequence from amplicon-based libraries.

@article{Hsu2015AmpliVarMD,
  title={AmpliVar: mutation detection in high-throughput sequence from amplicon-based libraries.},
  author={Arthur L. Hsu and Olga Kondrashova and Sebastian Lunke and Clare J. Love and Cliff J. Meldrum and Renate Marquis-Nicholson and Greg Corboy and Kym Pham and Matthew P. Wakefield and Paul M. Waring and G. R. Taylor},
  journal={Human mutation},
  year={2015},
  volume={36 4},
  pages={411-8}
}
Conventional means of identifying variants in high-throughput sequencing align each read against a reference sequence, and then call variants at each position. Here, we demonstrate an orthogonal means of identifying sequence variation by grouping the reads as amplicons prior to any alignment. We used AmpliVar to make key-value hashes of sequence reads and group reads as individual amplicons using a table of flanking sequences. Low-abundance reads were removed according to a selectable threshold… CONTINUE READING
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