TY - JOUR
T1 - Genozip
T2 - A universal extensible genomic data compressor
AU - Lan, Divon
AU - Tobler, Ray
AU - Souilmi, Yassine
AU - Llamas, Bastien
N1 - Publisher Copyright:
© 2021 The Author(s) 2021. Published by Oxford University Press.
PY - 2021/8/15
Y1 - 2021/8/15
N2 - We 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 widelyused 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.
AB - We 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 widelyused 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.
UR - http://www.scopus.com/inward/record.url?scp=85112047769&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btab102
DO - 10.1093/bioinformatics/btab102
M3 - Article
SN - 1367-4803
VL - 37
SP - 2225
EP - 2230
JO - Bioinformatics
JF - Bioinformatics
IS - 16
ER -