Introduction

Despite significant advancement in alignment algorithms, the exponential growth of nucleotide sequencing throughput threatens to outpace bioinformatic analysis. Computation may become the bottleneck of genome analysis if growing alignment costs are not mitigated by further improvement in algorithms. Much gain has been gleaned from indexing and compressing alignment databases, but many widely used alignment tools process input reads sequentially and are oblivious to any underlying redundancy in the reads themselves.Here we present Oculus, a software package that attaches to standard aligners and exploits read redundancy by performing streaming compression, alignment, and decompression of input sequences. This nearly lossless process (> 99.9%) led to alignment speedups of up to 270% across a variety of data sets, while requiring a modest amount of memory. We expect that streaming read compressors such as Oculus could become a standard addition to existing RNA-Seq and ChIP-Seq alignment pipelines, and potentially other applications in the future as throughput increases.Oculus efficiently condenses redundant input reads and wraps existing aligners to provide nearly identical SAM output in a fraction of the aligner runtime. It includes a number of useful features, such as tunable performance and fidelity options, compatibility with FASTA or FASTQ files, and adherence to the SAM format. The platform-independent C++ source code is freely available online, at http://code.google.com/p/oculus-bio.

Publications

  1. Oculus: faster sequence alignment by streaming read compression.
    Cite this
    Veeneman BA, Iyer MK, Chinnaiyan AM, 2012-11-01 - BMC bioinformatics

Credits

  1. Brendan A Veeneman
    Developer

    Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, United States of America

  2. Matthew K Iyer
    Developer

  3. Arul M Chinnaiyan
    Investigator

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Summary
AccessionBT000067
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++, Perl
User InterfaceTerminal Command Line
Download Count0
Submitted ByArul M Chinnaiyan