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Compact representation of k-mer de Bruijn graphs for genome read assembly

BMC Bioinformatics

Oct 25, 2013

Einar Andreas Rødland

Abstract

Processing of reads from high throughput sequencing is often done in terms of edges in the de Bruijn graph representing all k-mers from the reads. The memory requirements for storing all k-mers in a lookup table can be demanding, even after removal of read errors, but can be alleviated ...read more

Mentioned in this Paper

Severe Acute Respiratory Syndrome
Genome
Genomics
Sequencing
Sequence Determinations, DNA
DNA Sequence
23
65
Paper Details
References
  • References13
  • Citations5
12
  • References13
  • Citations5
1

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Compact representation of k-mer de Bruijn graphs for genome read assembly

BMC Bioinformatics

Oct 25, 2013

Einar Andreas Rødland

PMID: 24152242

DOI: 10.1186/1471-2105-14-313

Abstract

Processing of reads from high throughput sequencing is often done in terms of edges in the de Bruijn graph representing all k-mers from the reads. The memory requirements for storing all k-mers in a lookup table can be demanding, even after removal of read errors, but can be alleviated ...read more

Mentioned in this Paper

Severe Acute Respiratory Syndrome
Genome
Genomics
Sequencing
Sequence Determinations, DNA
DNA Sequence
23
65

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Viral Hemorrhagic Fevers

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.

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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SEQuel: improving the accuracy of genome assemblies

BioinformaticsJune 13, 2012
Roy RonenPavel Pevzner
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Readjoiner: a fast and memory efficient string graph-based sequence assembler

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Paper Details
References
  • References13
  • Citations5
12
  • References13
  • Citations5
1
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