Genozip

(available on Conda, Docker Hub and https://github.com/divonlan/genozip ; Documentation: http://genozip.com)

Genozip is a compressor for genomic files - while it can compress any file (i.e. not only genomic files), it is optimized to compress FASTQ, SAM/BAM/CRAM, VCF/BCF, FASTA, GVF, PHYLIP, Chain and 23andMe files.

Citing Do you find Genozip useful? Please cite:
Lan, D., et al. (2021) Genozip: a universal extensible genomic data compressor. Bioinformatics, https://doi.org/10.1093/bioinformatics/btab102
Lan, D., et al. (2020) genozip: a fast and efficient compression tool for VCF files Bioinformatics, 36, 4091–4092, https://doi.org/10.1093/bioinformatics/btaa290

Typically, a 2X-5X improvement over the existing compression is achieved when compressing already-compressed files like .fastq.gz .bam vcf.gz and much higher ratios in some other cases.

Yes, Genozip can compress already-compressed files (.gz .bz2 .xz .bam .cram).

The compression is lossless - the decompressed file is 100% identical to the original file (see documentation for exceptions).
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The command line options are similar to gzip and samtools/bcftools, so if you are familiar with these, it works pretty much the same. To get started, see: http://genozip.com

Genozip is free for non-commercial use. For a commercial license, please contact [email protected]

Usage is subject to terms and conditions. The non-commercial license can be viewed on http://genozip.com/license.html

THIS SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.