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Turtle: identifying frequent k-mers with cache-efficient algorithms

Bioinformatics

Mar 13, 2014

Rajat Shuvro RoyAlexander Schliep

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Abstract

Counting the frequencies of k-mers in read libraries is often a first step in the analysis of high-throughput sequencing data. Infrequent k-mers are assumed to be a result of sequencing errors. The frequent k-mers constitute a reduced but error-free representation of the experiment, whi...read more

Mentioned in this Paper

Severe Acute Respiratory Syndrome
Genome
Bio-Informatics
Computer Programs and Programming
Sequencing
Sequence Determinations, DNA
High-Throughput Nucleotide Sequencing
Genome, Human
17
83
Paper Details
References
  • References15
  • Citations13
12
  • References15
  • Citations13
12

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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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Turtle: identifying frequent k-mers with cache-efficient algorithms

Bioinformatics

Mar 13, 2014

Rajat Shuvro RoyAlexander Schliep

PMID: 24618471

DOI: 10.1093/bioinformatics/btu132

Abstract

Counting the frequencies of k-mers in read libraries is often a first step in the analysis of high-throughput sequencing data. Infrequent k-mers are assumed to be a result of sequencing errors. The frequent k-mers constitute a reduced but error-free representation of the experiment, whi...read more

Mentioned in this Paper

Severe Acute Respiratory Syndrome
Genome
Bio-Informatics
Computer Programs and Programming
Sequencing
Sequence Determinations, DNA
High-Throughput Nucleotide Sequencing
Genome, Human
17
83

Feeds With Similar Papers

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 (ASM)

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.

Related Papers

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Repeat-aware modeling and correction of short read errors

BMC BioinformaticsMarch 5, 2011
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BMC BioinformaticsAugust 13, 2011
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Paper Details
References
  • References15
  • Citations13
12
  • References15
  • Citations13
12

Download from

Publisher
PubMed
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