title: A fast sequence assembly method based on compressed data structures.
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 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.
authors.forename: Peifeng
authors.initials: P
authors.lastname: Liang
authors.forename: Yancong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Kui
authors.initials: K
authors.lastname: Lin
authors.forename: Jinglu
authors.initials: J
authors.lastname: Hu
mesh_terms: D000465:Algorithms; D044962:Data Compression; D030541:Databases, Genetic; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial; D017422:Sequence Analysis, DNA / Q000379:methods*; D013302:Streptomyces / Q000235:genetics