deGSM: memory scalable construction of large scale de Bruijn Graph
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 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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Sequences generated by maximum-period nonlinear feedback shift registers are known as de Bruijn sequences. The problem of designing de Bruijn sequences has received considerable attention. There is only one full cycle in the state graph of de Bruijn sequences. Most popular algorithms for generating de Bruijn sequences start from a nonsingular linear feedback shift register producing several sho...
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Searching for other participants is one of the most important operations in a distributed system. We are interested in topologies in which it is possible to route a packet in a fixed number of hops until it arrives at its destination. Given a constant d, this paper introduces a new self-stabilizing protocol for the q-ary d-dimensional de Bruijn graph (q = d √ n) that is able to route any search...
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ژورنال
عنوان ژورنال: IEEE/ACM Transactions on Computational Biology and Bioinformatics
سال: 2019
ISSN: 1545-5963,1557-9964,2374-0043
DOI: 10.1109/tcbb.2019.2913932