Performance analysis of parallel de novo genome assembly in shared memory system
نویسندگان
چکیده
منابع مشابه
Performance Characterization of De Novo Genome Assembly on Leading Parallel Systems
De novo genome assembly is one of the most important and challenging computational problems in modern genomics; further, it shares algorithms and communication patterns important to other graph analytic and irregular applications. Unlike simulations, it has no floating point arithmetic and is dominated by small memory transactions within and between computing nodes. In this work, we focus on th...
متن کاملRAMPART: a workflow management system for de novo genome assembly
MOTIVATION The de novo assembly of genomes from whole- genome shotgun sequence data is a computationally intensive, multi-stage task and it is not known a priori which methods and parameter settings will produce optimal results. In current de novo assembly projects, a popular strategy involves trying many approaches, using different tools and settings, and then comparing and contrasting the res...
متن کاملClustering of Short Read Sequences for de novo Transcriptome Assembly
Given the importance of transcriptome analysis in various biological studies and considering thevast amount of whole transcriptome sequencing data, it seems necessary to develop analgorithm to assemble transcriptome data. In this study we propose an algorithm fortranscriptome assembly in the absence of a reference genome. First, the contiguous sequencesare generated using de Bruijn graph with d...
متن کاملScalable De Novo Genome Assembly Using Pregel
De novo genome assembly is the process of stitching short DNA sequences to generate longer DNA sequences, without using any reference sequence for alignment. It enables highthroughput genome sequencing and thus accelerates the discovery of new genomes. In this paper, we present a toolkit, called PPA-assembler, for de novo genome assembly in a distributed setting. The operations in our toolkit p...
متن کاملDe Novo Assembly with the Genome Analyzer
The utility of the Illumina Genome Analyzer for a broad range of applications is evidenced by an amazing rate of publication by the research community1. In addition to human-scale resequencing2 –4 and other applications requiring a reference genome, researchers are performing de novo assembly. Several important organisms have been sequenced for the first time as a direct result of the consisten...
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: IOP Conference Series: Earth and Environmental Science
سال: 2018
ISSN: 1755-1315
DOI: 10.1088/1755-1315/187/1/012032