Dynamic compression schemes for graph coloring

Bioinformatics
Harun MustafaAndré Kahles

Abstract

Technological advancements in high-throughput DNA sequencing have led to an exponential growth of sequencing data being produced and stored as a byproduct of biomedical research. Despite its public availability, a majority of this data remains hard to query for the research community due to a lack of efficient data representation and indexing solutions. One of the available techniques to represent read data is a condensed form as an assembly graph. Such a representation contains all sequence information but does not store contextual information and metadata. We present two new approaches for a compressed representation of a graph coloring: a lossless compression scheme based on a novel application of wavelet tries as well as a highly accurate lossy compression based on a set of Bloom filters. Both strategies retain a coloring even when adding to the underlying graph topology. We present construction and merge procedures for both methods and evaluate their performance on a wide range of different datasets. By dropping the requirement of a fully lossless compression and using the topological information of the underlying graph, we can reduce memory requirements by up to three orders of magnitude. Representing individual colors as...Continue Reading

References

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Citations

Mar 16, 2019·Bioinformatics·Guillaume PagèsSergei Grudinin
Jan 1, 2020·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Mikhail KarasikovAndré Kahles
Mar 17, 2020·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Fatemeh AlmodaresiRob Patro
Sep 13, 2019·Bioinformatics·Martin D MuggliChristina Boucher
Dec 18, 2020·Genome Research·Camille MarchetRayan Chikhi
Sep 11, 2019·Bioinformatics·Robert S Harris, Paul Medvedev
Jul 13, 2021·Bioinformatics·Daniel DanciuGunnar Rätsch
May 29, 2020·Bioinformatics·Bahar AlipanahiChristina Boucher

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Software Mentioned

bzip2
VARI
RBF
gzip
Rainbowfish
SDSL
deBGR

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