Indexing k-mers in Linear-space for Quality Value Compression

Yoshihiro Shibuya, Yoshihiro Shibuya, Matteo Comin

2019

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.

Paper Citation

in Harvard Style

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 (BIOSTEC 2019) - Volume 3: BIOINFORMATICS; ISBN 978-989-758-353-7, SciTePress, pages 21-29. DOI: 10.5220/0007369100210029

in Bibtex Style

@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 (BIOSTEC 2019) - Volume 3: BIOINFORMATICS},
year={2019},
pages={21-29},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0007369100210029},
isbn={978-989-758-353-7},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - Volume 3: 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
PB - SciTePress