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Efficient counting of k-mers in DNA sequences using a bloom filter

BMC Bioinformatics

Aug 13, 2011

Páll Melsted, Jonathan K Pritchard

Abstract

Counting k-mers (substrings of length k in DNA sequence data) is an essential component of many methods in bioinformatics, including for genome and transcriptome assembly, for metagenomic sequencing, and for error correction of sequence reads. Although simple in principle, counting k-me...read more

Mentioned in this Paper

Chromosomes, Human, Pair 21
Severe Acute Respiratory Syndrome
Jellyfish
HapMap
Genome
Genome Assembly Sequence
Bio-Informatics
Computer Programs and Programming
Pandas, Giant
Sequence Determinations, DNA
5
274
Paper Details
References
  • References16
  • Citations44
12
  • References16
  • Citations44
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Efficient counting of k-mers in DNA sequences using a bloom filter

BMC Bioinformatics

Aug 13, 2011

Páll Melsted, Jonathan K Pritchard

PMID: 21831268

DOI: 10.1186/1471-2105-12-333

Abstract

Counting k-mers (substrings of length k in DNA sequence data) is an essential component of many methods in bioinformatics, including for genome and transcriptome assembly, for metagenomic sequencing, and for error correction of sequence reads. Although simple in principle, counting k-me...read more

Mentioned in this Paper

Chromosomes, Human, Pair 21
Severe Acute Respiratory Syndrome
Jellyfish
HapMap
Genome
Genome Assembly Sequence
Bio-Informatics
Computer Programs and Programming
Pandas, Giant
Sequence Determinations, DNA
5
274

Feeds With Similar Papers

Stanford Department of Genetics

Find the latest research from the Stanford Medicine Department of Genetics here.

Structural Biology: Biophysics

Structural Biology: Biophysics describes the study of structural biology using various biophysical techiniques such as imaging, computational modeling, etc. Discover the latest research on structrual biology here.

Related Papers

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Paper Details
References
  • References16
  • Citations44
12
  • References16
  • Citations44
12345

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