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Indexing Arbitrary-Length k-Mers in Sequencing Reads

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 a...

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Détails bibliographiques
Publié dans:PLoS One
Auteurs principaux: Kowalski, Tomasz, Grabowski, Szymon, Deorowicz, Sebastian
Format: Artigo
Langue:Inglês
Publié: Public Library of Science 2015
Sujets:
Accès en ligne:https://ncbi.nlm.nih.gov/pmc/articles/PMC4504488/
https://ncbi.nlm.nih.gov/pubmed/26182400
https://ncbi.nlm.nih.govhttp://dx.doi.org/10.1371/journal.pone.0133198
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