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» Assembly of Large Genomes from Paired Short Reads
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BMCBI
2008
220views more  BMCBI 2008»
13 years 5 months ago
Gene prediction in metagenomic fragments: A large scale machine learning approach
Background: Metagenomics is an approach to the characterization of microbial genomes via the direct isolation of genomic sequences from the environment without prior cultivation. ...
Katharina J. Hoff, Maike Tech, Thomas Lingner, Rol...
BMCBI
2011
12 years 11 months ago
Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies
Background: Next-generation sequencing technologies allow genomes to be sequenced more quickly and less expensively than ever before. However, as sequencing technology has improve...
Joshua Wetzel, Carl Kingsford, Mihai Pop
BMCBI
2007
151views more  BMCBI 2007»
13 years 5 months ago
Minimus: a fast, lightweight genome assembler
Background: Genome assemblers have grown very large and complex in response to the need for algorithms to handle the challenges of large whole-genome sequencing projects. Many of ...
Daniel D. Sommer, Arthur L. Delcher, Steven L. Sal...
FPL
2010
Springer
188views Hardware» more  FPL 2010»
13 years 3 months ago
SeqHive: A Reconfigurable Computer Cluster for Genome Re-sequencing
We demonstrate how Field Programmable Gate Arrays (FPGAs) may be used to address the computing challenges associated with assembling genome sequences from recent ultra-high-through...
Kristian Stevens, Henry Chen, Terry Filiba, Peter ...
BMCBI
2010
189views more  BMCBI 2010»
13 years 5 months ago
Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs
Background: Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly probl...
Vamsi Kundeti, Sanguthevar Rajasekaran, Hieu Dinh,...