A fast sequence assembly method based on compressed data structures

Peifeng Liang, Yancong Zhang, Kui Lin, Takayuki Furuzuki

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Assembling a large genome using next generation sequencing reads requires large computer memory and a long execution time. To reduce these requirements, a memory and time efficient assembler is presented from applying FM-index in JR-Assembler, called FMJ-Assembler, where FM stand for FM<inf>R</inf>-index derived from the FM-index and BWT and J for jumping extension. The FMJ-Assembler uses expanded FM-index and BWT to compress data of reads to save memory and jumping extension method make it faster in CPU time. An extensive comparison of the FMJ-Assembler with current assemblers shows that the FMJ-Assembler achieves a better or comparable overall assembly quality and requires lower memory use and less CPU time. All these advantages of the FMJ-Assembler indicate that the FMJ-Assembler will be an efficient assembly method in next generation sequencing technology.

Original languageEnglish
Title of host publication2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages326-329
Number of pages4
ISBN (Print)9781424479290
DOIs
Publication statusPublished - 2014 Nov 2
Event2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014 - Chicago, United States
Duration: 2014 Aug 262014 Aug 30

Other

Other2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014
CountryUnited States
CityChicago
Period14/8/2614/8/30

ASJC Scopus subject areas

  • Health Informatics
  • Computer Science Applications
  • Biomedical Engineering

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  • Cite this

    Liang, P., Zhang, Y., Lin, K., & Furuzuki, T. (2014). A fast sequence assembly method based on compressed data structures. In 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014 (pp. 326-329). [6943595] Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/EMBC.2014.6943595