MersV1, Main, Exploration, bibRecord, 000804

Squeakr: an exact and approximate k-mer counting system.

Identifieur interne : 000804 ( Main/Exploration ); précédent : 000803; suivant : 000805

Squeakr: an exact and approximate k-mer counting system.

Auteurs : Prashant Pandey [États-Unis] ; Michael A. Bender [États-Unis] ; Rob Johnson [États-Unis] ; Rob Patro [États-Unis] ; Bonnie Berger

Source :

Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2018.

RBID : pubmed:29444235

Descripteurs français

KwdFr :
- Algorithmes, Analyse de profil d'expression de gènes (), Analyse de séquence d'ADN (), Analyse de séquence d'ARN (), Animaux, Eucaryotes (génétique), Génome, Génomique (), Humains, Logiciel, Séquençage nucléotidique à haut débit ().
MESH :
- génétique : Eucaryotes.
- Algorithmes, Analyse de profil d'expression de gènes, Analyse de séquence d'ADN, Analyse de séquence d'ARN, Animaux, Génome, Génomique, Humains, Logiciel, Séquençage nucléotidique à haut débit.

English descriptors

KwdEn :
- Algorithms, Animals, Eukaryota (genetics), Gene Expression Profiling (methods), Genome, Genomics (methods), High-Throughput Nucleotide Sequencing (methods), Humans, Sequence Analysis, DNA (methods), Sequence Analysis, RNA (methods), Software.
MESH :
- genetics : Eukaryota.
- methods : Gene Expression Profiling, Genomics, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Sequence Analysis, RNA.
- Algorithms, Animals, Genome, Humans, Software.

Abstract

k-mer-based algorithms have become increasingly popular in the processing of high-throughput sequencing data. These algorithms span the gamut of the analysis pipeline from k-mer counting (e.g. for estimating assembly parameters), to error correction, genome and transcriptome assembly, and even transcript quantification. Yet, these tasks often use very different k-mer representations and data structures. In this article, we show how to build a k-mer-counting and multiset-representation system using the counting quotient filter, a feature-rich approximate membership query data structure. We introduce the k-mer-counting/querying system Squeakr (Simple Quotient filter-based Exact and Approximate Kmer Representation), which is based on the counting quotient filter. This off-the-shelf data structure turns out to be an efficient (approximate or exact) representation for sets or multisets of k-mers.

DOI: 10.1093/bioinformatics/btx636
PubMed: 29444235

Affiliations:

Le document en format XML

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<front><div type="abstract" xml:lang="en">k-mer-based algorithms have become increasingly popular in the processing of high-throughput sequencing data. These algorithms span the gamut of the analysis pipeline from k-mer counting (e.g. for estimating assembly parameters), to error correction, genome and transcriptome assembly, and even transcript quantification. Yet, these tasks often use very different k-mer representations and data structures. In this article, we show how to build a k-mer-counting and multiset-representation system using the counting quotient filter, a feature-rich approximate membership query data structure. We introduce the k-mer-counting/querying system Squeakr (Simple Quotient filter-based Exact and Approximate Kmer Representation), which is based on the counting quotient filter. This off-the-shelf data structure turns out to be an efficient (approximate or exact) representation for sets or multisets of k-mers.</div>
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Serveur d'exploration MERS

Squeakr: an exact and approximate k-mer counting system.

Squeakr: an exact and approximate k-mer counting system.

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki

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