Abstract
BackgroundThe alignment of short reads generated by next-generation sequencers to genomes is an important problem in many biomedical and bioinformatics applications. Although many proposed methods work very well on narrow ranges of read lengths, they tend to suffer in performance and alignment quality for reads outside of these ranges.ResultsWe introduce RandAL, a novel method that aligns DNA sequences to reference genomes. Our approach utilizes two FM indices to facilitate efficient bidirectional searching, a pruning heuristic to speed up the computing of edit distances, and most importantly, a randomized strategy that enables effective estimation of key parameters. Extensive comparisons showed that RandAL outperformed popular aligners in most instances and was unique in its consistent and accurate performance over a wide range of read lengths and error rates. The software package is publicly available at https://github.com/namsyvo/RandAL.ConclusionsRandAL promises to align effectively and accurately short reads that come from a variety of technologies with different read lengths and rates of sequencing error.
Highlights
The alignment of short reads generated by next-generation sequencers to genomes is an important problem in many biomedical and bioinformatics applications
Bowtie uses the Burrows-Wheeler Transform (BWT) and FM index to build a permanent index of the reference genome
Burrows-Wheeler Alignment (BWA)-SW exploits the BWT and several heuristics to speed up the local alignment of reads
Summary
The alignment of short reads generated by next-generation sequencers to genomes is an important problem in many biomedical and bioinformatics applications. The alignment of reads to genomes is an important problem in many biomedical applications that relied on next-generation sequencing technologies. Since one expects genomes within the same species differ little, such “referenced” genomes can facilitate the assembly of new genomes of other individuals within the same species from short reads To address this problem, researchers have proposed many approaches together with software packages. On the many existing algorithms struggle to perform consistently across a wide range of read lengths. Methods such as Bowtie [1] and Burrows-Wheeler Alignment (BWA) [2] tend to perform better with shorter reads. BWA-SW exploits the BWT and several heuristics to speed up the local alignment of reads
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