A fast sequence assembly method based on compressed data structures

Peifeng Liang, Yancong Zhang, Kui Lin, Jinglu Hu

研究成果: Conference contribution

抄録

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 FMR-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.

本文言語English
ホスト出版物のタイトル2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014
出版社Institute of Electrical and Electronics Engineers Inc.
ページ326-329
ページ数4
ISBN(電子版)9781424479290
DOI
出版ステータスPublished - 2014 11 2
イベント2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014 - Chicago, United States
継続期間: 2014 8 262014 8 30

出版物シリーズ

名前2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014

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
  • Medicine(all)

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