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Authors: Yoshihiro Shibuya 1 and Matteo Comin 2

Affiliations: 1 Department of Information Engineering, University of Padua, via Gradenigo 6B, Padua, Italy, Laboratoire d’Informatique Gaspard-Monge (LIGM), University Paris-Est Marne-la-Vallée, Bâtiment Copernic - 5, bd Descartes, Champs sur Marne and France ; 2 Department of Information Engineering, University of Padua, via Gradenigo 6B, Padua and Italy

ISBN: 978-989-758-353-7

Keyword(s): k-mers, Indexing, Quality Score, Read Compression.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Next Generation Sequencing ; Sequence Analysis

Abstract: Many bioinformatics tools heavily rely on k-mer dictionaries to describe the composition of sequences and allow for faster reference-free algorithms or look-ups. Unfortunately, naive k-mer dictionaries are very memory inefficient, requiring very large amount of storage space to save each k-mer. This problem is generally worsened by the necessity of an index for fast queries. In this work we discuss how to build an indexed linear reference containing a set of input k-mers, and its application to the compression of quality score in FASTQ files. Most of the entropy of sequencing data lies in the quality scores, and thus they are difficult to compress. Here, we present an application to improve the compressibility of quality values while preserving the information for SNPs calling. We show how a dictionary of significant k-mers, obtained from SNPs databases and multiple genomes, can be indexed in linear space and used to improve the compression of quality value. Availability: the software is freely available at https://github.com/yhhshb/yalff. (More)

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Paper citation in several formats:
Shibuya, Y. and Comin, M. (2019). Indexing k-mers in Linear-space for Quality Value Compression.In Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3 BIOINFORMATICS: BIOINFORMATICS, ISBN 978-989-758-353-7, pages 21-29. DOI: 10.5220/0007369100210029

@conference{bioinformatics19,
author={Yoshihiro Shibuya. and Matteo Comin.},
title={Indexing k-mers in Linear-space for Quality Value Compression},
booktitle={Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3 BIOINFORMATICS: BIOINFORMATICS,},
year={2019},
pages={21-29},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0007369100210029},
isbn={978-989-758-353-7},
}

TY - CONF

JO - Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3 BIOINFORMATICS: BIOINFORMATICS,
TI - Indexing k-mers in Linear-space for Quality Value Compression
SN - 978-989-758-353-7
AU - Shibuya, Y.
AU - Comin, M.
PY - 2019
SP - 21
EP - 29
DO - 10.5220/0007369100210029

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