genozip: a fast and efficient compression tool for VCF files

Divon Lan; Raymond Tobler; Yassine Souilmi; Bastien Llamas

doi:10.1093/bioinformatics/btaa290

genozip: a fast and efficient compression tool for VCF files

Bioinformatics. 2020 Jul 1;36(13):4091-4092. doi: 10.1093/bioinformatics/btaa290.

Authors

Divon Lan¹, Raymond Tobler¹, Yassine Souilmi¹, Bastien Llamas¹

Affiliation

¹ School of Biological Sciences, The Environment Institute, Faculty of Sciences, The University of Adelaide, Adelaide, SA 5005, Australia.

Abstract

Motivation: genozip is a new lossless compression tool for Variant Call Format (VCF) files. By applying field-specific algorithms and fully utilizing the available computational hardware, genozip achieves the highest compression ratios amongst existing lossless compression tools known to the authors, at speeds comparable with the fastest multi-threaded compressors.

Availability and implementation: genozip is freely available to non-commercial users. It can be installed via conda-forge, Docker Hub, or downloaded from github.com/divonlan/genozip.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Data Compression*
Genomics
High-Throughput Nucleotide Sequencing*
Software