TY - GEN
T1 - A fast sequence assembly method based on compressed data structures
AU - Liang, Peifeng
AU - Zhang, Yancong
AU - Lin, Kui
AU - Hu, Jinglu
N1 - Publisher Copyright:
© 2014 IEEE.
PY - 2014/11/2
Y1 - 2014/11/2
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84929468237&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84929468237&partnerID=8YFLogxK
U2 - 10.1109/EMBC.2014.6943595
DO - 10.1109/EMBC.2014.6943595
M3 - Conference contribution
C2 - 25569963
AN - SCOPUS:84929468237
T3 - 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014
SP - 326
EP - 329
BT - 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014
PB - Institute of Electrical and Electronics Engineers Inc.
T2 - 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014
Y2 - 26 August 2014 through 30 August 2014
ER -