Scalable Genome Assembly through Parallel de Bruijn Graph Construction for Multiple k-mers
نویسندگان
چکیده
منابع مشابه
GPU-Accelerated Bidirected De Bruijn Graph Construction for Genome Assembly
De Bruijn graph construction is a basic component in de novo genome assembly for short reads generated from the second-generation sequencing machines. As this component processes a large amount of data and performs intensive computation, we propose to use the GPU (Graphics Processing Unit) for acceleration. Specifically, we propose a staged algorithm to utilize the GPU for computation over larg...
متن کاملDe Bruijn Graph based De novo Genome Assembly
The Next Generation Sequencing (NGS) is an important process which assures inexpensive organization of vast size of raw sequence data set over any traditional sequencing systems or methods. Various aspects of NGS like template preparation, sequencing imaging and genome alignment and assembly outlines the genome sequencing and alignment .Consequently, deBruijn Graph (dBG) is an important mathema...
متن کاملHaVec: An Efficient de Bruijn Graph Construction Algorithm for Genome Assembly
BACKGROUND The rapid advancement of sequencing technologies has made it possible to regularly produce millions of high-quality reads from the DNA samples in the sequencing laboratories. To this end, the de Bruijn graph is a popular data structure in the genome assembly literature for efficient representation and processing of data. Due to the number of nodes in a de Bruijn graph, the main barri...
متن کاملImproved Parallel Processing of Massive De Bruijn Graph for Genome Assembly
De Bruijn graph is a vastly used technique for developing genome assembly software nowadays. The scale of this kind of graph can reach billions of vertices and edges which poses great challenges to the genome assembly task. It is of great importance to study scalable genome assembly algorithms in order to cope with this situation. Despite some recent works which begin to address the scalability...
متن کاملMemory Efficient De Bruijn Graph Construction
Massively parallel DNA sequencing technologies are revolutionizing genomics research. Billions of short reads generated at low costs can be assembled for reconstructing the whole genomes. Unfortunately, the large memory footprint of the existing de novo assembly algorithms makes it challenging to get the assembly done for higher eukaryotes like mammals. In this work, we investigate the memory i...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Scientific Reports
سال: 2019
ISSN: 2045-2322
DOI: 10.1038/s41598-019-51284-9