sBWT

The software tool sBWT proposes a new hardware-parallelizable indexing and matching approach for fast string matching in large genomes or sequencing reads. The tool is based on a BWT variant called the Schindler transform, which can be built with simplified hardware-acceleration-friendly algorithms. The implementation achieves significant speedups in indexing and searching and is available in C++ with CPU-only and GPU-accelerated versions.

Topic

Sequencing;DNA;Sequence analysis

Detail

  • Operation: Sequence analysis;Genome indexing;Sequence alignment

  • Software interface: Command-line user interface

  • Language: C++

  • License: Not stated

  • Cost: Free

  • Version name: v1.0-beta.1

  • Credit: National Science Council of Taiwan.

  • Input: -

  • Output: -

  • Contact: juihunghung@gmail.com, Min-Te Chou poi5305@gmail.com, Ting-Wei Hong thestyle1202@gmail.com, Chia-Hua Chang CHChang810716@gmail.com

  • Collection: -

  • Maturity: -

Publications

  • sBWT: memory efficient implementation of the hardware-acceleration-friendly Schindler transform for the fast biological sequence mapping.
  • Chang CH, et al. sBWT: memory efficient implementation of the hardware-acceleration-friendly Schindler transform for the fast biological sequence mapping. sBWT: memory efficient implementation of the hardware-acceleration-friendly Schindler transform for the fast biological sequence mapping. 2016; 32:3498-3500. doi: 10.1093/bioinformatics/btw419
  • https://doi.org/10.1093/bioinformatics/btw419
  • PMID: 27412087
  • PMC: -

Download and documentation

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