Apr 18, 2013

CGAP-align: a high performance DNA short read alignment tool

PloS One
Yaoliang ChenRui Chen

Abstract

Next generation sequencing platforms have greatly reduced sequencing costs, leading to the production of unprecedented amounts of sequence data. BWA is one of the most popular alignment tools due to its relatively high accuracy. However, mapping reads using BWA is still the most time consuming step in sequence analysis. Increasing mapping efficiency would allow the community to better cope with ever expanding volumes of sequence data. We designed a new program, CGAP-align, that achieves a performance improvement over BWA without sacrificing recall or precision. This is accomplished through the use of Suffix Tarray, a novel data structure combining elements of Suffix Array and Suffix Tree. We also utilize a tighter lower bound estimation for the number of mismatches in a read, allowing for more effective pruning during inexact mapping. Evaluation of both simulated and real data suggests that CGAP-align consistently outperforms the current version of BWA and can achieve over twice its speed under certain conditions, all while obtaining nearly identical results. CGAP-align is a new time efficient read alignment tool that extends and improves BWA. The increase in alignment speed will be of critical assistance to all sequence-based ...Continue Reading

Mentioned in this Paper

Biologic Segmentation
Computer Programs and Programming
Sequencing
Massively-Parallel Sequencing
Base Pairing
High-Throughput Nucleotide Sequencing
Suffix brand of benzoylprop-ethyl
Genome, Human
Metric
Determination, Sequence Homology

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