Genozip - a universal extensible genomic data compressor

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dc.contributor.authorLan, D.
dc.contributor.authorTobler, R.
dc.contributor.authorSouilmi, Y.
dc.contributor.authorLlamas, B.
dc.contributor.editorKelso, J.
dc.date.issued2021
dc.description.abstractWe present Genozip, a universal and fully featured compression software for genomic data. Genozip is designed to be a general-purpose software and a development framework for genomic compression by providing five core capabilities - universality (support for all common genomic file formats), high compression ratios, speed, feature-richness, and extensibility. Genozip delivers high-performance compression for widely-used genomic data formats in genomics research, namely FASTQ, SAM/BAM/CRAM, VCF, GVF, FASTA, PHYLIP, and 23andMe formats. Our test results show that Genozip is fast and achieves greatly improved compression ratios, even when the files are already compressed. Further, Genozip is architected with a separation of the Genozip Framework from file-format-specific Segmenters and data-type-specific Codecs. With this, we intend for Genozip to be a general-purpose compression platform where researchers can implement compression for additional file formats, as well as new codecs for data types or fields within files, in the future. We anticipate that this will ultimately increase the visibility and adoption of these algorithms by the user community, thereby accelerating further innovation in this space. Availability: Genozip is written in C. The code is open-source and available on GitHub (https://github.com/divonlan/genozip). The package is free for non-commercial use. It is distributed as a Docker container on DockerHub and through the conda package manager. Genozip is tested on Linux, Mac, and Windows. Supplementary information: Supplementary data are available at Bioinformatics online.
dc.description.statementofresponsibilityDivon Lan, Ray Tobler, Yassine Souilmi, Bastien Llamas
dc.identifier.citationBioinformatics, 2021; 37(16):2225-2230
dc.identifier.doi10.1093/bioinformatics/btab102
dc.identifier.issn1367-4803
dc.identifier.issn1367-4811
dc.identifier.orcidLan, D. [0000-0002-9794-6825]
dc.identifier.orcidTobler, R. [0000-0002-4603-1473]
dc.identifier.orcidSouilmi, Y. [0000-0001-7543-4864]
dc.identifier.orcidLlamas, B. [0000-0002-5550-9176]
dc.identifier.urihttps://hdl.handle.net/2440/132569
dc.language.isoen
dc.publisherOxford University Press
dc.relation.granthttp://purl.org/au-research/grants/arc/DE190101069
dc.relation.granthttp://purl.org/au-research/grants/arc/FT170100448
dc.relation.granthttp://purl.org/au-research/grants/arc/DP190103705
dc.rights© The Author(s) 2021. Published by Oxford University Press. 2225 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.source.urihttps://doi.org/10.1093/bioinformatics/btab102
dc.titleGenozip - a universal extensible genomic data compressor
dc.typeJournal article
pubs.publication-statusPublished

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