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Exploiting sparseness in de novo genome assembly

BMC Bioinformatics

May 2, 2012

Chengxi YeDouglas W Yu

Abstract

The very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments. In this paper, we demonstrate that constructing a sparse assembly graph which stores only a small fraction of the observed k-m...read more

Mentioned in this Paper

Severe Acute Respiratory Syndrome
Alkalescens-Dispar Group
Genome
Genome Assembly Sequence
Computer Programs and Programming
Sequence Determinations, DNA
High-Throughput Nucleotide Sequencing
Computer Storage Devices
Genome, Human
12
1
158
Paper Details
References
  • References27
  • Citations51
123
  • References27
  • Citations51
12345...

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Exploiting sparseness in de novo genome assembly

BMC Bioinformatics

May 2, 2012

Chengxi YeDouglas W Yu

PMID: 22537038

DOI: 10.1186/1471-2105-13-s6-s1

Abstract

The very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments. In this paper, we demonstrate that constructing a sparse assembly graph which stores only a small fraction of the observed k-m...read more

Mentioned in this Paper

Severe Acute Respiratory Syndrome
Alkalescens-Dispar Group
Genome
Genome Assembly Sequence
Computer Programs and Programming
Sequence Determinations, DNA
High-Throughput Nucleotide Sequencing
Computer Storage Devices
Genome, Human
12
1
158

Feeds With Similar Papers

Severe Acute Respiratory Syndrome

Severe acute respiratory syndrome (SARS) is a viral respiratory disease of zoonotic origin caused by the SARS coronavirus (SARS-CoV). Initial symptoms are flu-like and may include fever, muscle pain, lethargy symptoms, cough, sore throat, and other nonspecific symptoms. SARS may eventually lead to shortness of breath and pneumonia; either direct viral pneumonia or secondary bacterial pneumonia. DIscover the latest research on SARS here.

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Viral Hemorrhagic Fevers caused by ebola, marburg and lassa viruses often manifest as multiple organ dysfunction and hemorrhagic shock with high mortality. Discover the latest research on Viral Hemorrhagic Fevers here.

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Succinct data structures for assembling large genomes

BioinformaticsJanuary 20, 2011
Thomas C Conway, Andrew J Bromage
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Efficient de novo assembly of large genomes using compressed data structures

Genome ResearchDecember 14, 2011
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Paper Details
References
  • References27
  • Citations51
123
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  • Citations51
12345...

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