MBG: Minimizer-based sparse de Bruijn Graph construction
نویسندگان
چکیده
منابع مشابه
Memory 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...
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de Bruijn graph-based algorithms are one of the two most widely used approaches for de novo genome assembly. A major limitation of this approach is the large computational memory space requirement to construct the de Bruijn graph, which scales with k-mer length and total diversity (N) of unique k-mers in the genome expressed in base pairs or roughly (2k+8)N bits. This limitation is particularly...
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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...
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This paper presents a method to find new de Bruijn cycles based on ones of lesser order. This is done by mapping a de Bruijn cycle to several vertex disjoint cycles in a de Bruijn digraph of higher order and connecting these cycles into one full cycle. We characterize homomorphisms between de Bruijn digraphs of different orders that allow this construction. These maps generalize the well-known ...
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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...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2021
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btab004