AmpliVar: Mutation detection in high-throughput sequence from Amplicon-Based Libraries
Details
Publication Year 2015-04,Volume 36,Issue #4,Page 411-8
Journal Title
Hum Mutat
Publication Type
Journal Article
Abstract
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.
Publisher
Wiley
Research Division(s)
Bioinformatics
PubMed ID
25664426
Terms of Use/Rights Notice
Refer to copyright notice on published article.


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