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AmpliVar: Mutation detection in high-throughput sequence from Amplicon-Based Libraries


Hsu, AL; Kondrashova, O; Lunke, S; Love, CJ; Meldrum, C; Marquis-Nicholson, R; Corboy, G; Pham, K; Wakefield, M; Waring, PM; Taylor, GR
2015-04
Hum Mutat
Journal Article
36
4
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, and reads above this threshold were aligned as groups, rather than as individual reads, permitting the use of sensitive alignment tools. We show that this approach is more sensitive, more specific, and more computationally efficient than comparable methods for the analysis of amplicon-based high-throughput sequencing data. The method can be extended to enable alignment-free confirmation of variants seen in hybridization capture target-enrichment data.
Wiley
Bioinformatics
10.1002/humu.22763
25664426
Refer to copyright notice on published article.

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Creation Date 2015-05-21 11:10:22 Last Modified 2015-05-21 11:12:05