MersV1, PubMed, Corpus, bibRecord, 001552

Indexing Arbitrary-Length k-Mers in Sequencing Reads.

Identifieur interne : 001552 ( PubMed/Corpus ); précédent : 001551; suivant : 001553

Indexing Arbitrary-Length k-Mers in Sequencing Reads.

Auteurs : Tomasz Kowalski ; Szymon Grabowski ; Sebastian Deorowicz

Source :

PloS one [ 1932-6203 ] ; 2015.

RBID : pubmed:26182400

English descriptors

KwdEn :
- Algorithms, Animals, Caenorhabditis elegans (genetics), Datasets as Topic, Escherichia coli (genetics), Genome, High-Throughput Nucleotide Sequencing, Humans, Sequence Analysis, RNA (methods), Sequence Analysis, RNA (statistics & numerical data), Software.
MESH :
- genetics : Caenorhabditis elegans, Escherichia coli.
- methods : Sequence Analysis, RNA.
- statistics & numerical data : Sequence Analysis, RNA.
- Algorithms, Animals, Datasets as Topic, Genome, High-Throughput Nucleotide Sequencing, Humans, Software.

Abstract

We propose a lightweight data structure for indexing and querying collections of NGS reads data in main memory. The data structure supports the interface proposed in the pioneering work by Philippe et al. for counting and locating k-mers in sequencing reads. Our solution, PgSA (pseudogenome suffix array), based on finding overlapping reads, is competitive to the existing algorithms in the space use, query times, or both. The main applications of our index include variant calling, error correction and analysis of reads from RNA-seq experiments.

DOI: 10.1371/journal.pone.0133198
PubMed: 26182400

Links to Exploration step

pubmed:26182400

Le document en format XML

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<author><name sortKey="Grabowski, Szymon" sort="Grabowski, Szymon" uniqKey="Grabowski S" first="Szymon" last="Grabowski">Szymon Grabowski</name>
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<front><div type="abstract" xml:lang="en">We propose a lightweight data structure for indexing and querying collections of NGS reads data in main memory. The data structure supports the interface proposed in the pioneering work by Philippe et al. for counting and locating k-mers in sequencing reads. Our solution, PgSA (pseudogenome suffix array), based on finding overlapping reads, is competitive to the existing algorithms in the space use, query times, or both. The main applications of our index include variant calling, error correction and analysis of reads from RNA-seq experiments. </div>
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Indexing Arbitrary-Length k-Mers in Sequencing Reads.

Indexing Arbitrary-Length k-Mers in Sequencing Reads.

Source :

English descriptors

Abstract

Links to Exploration step

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