genozip is a compressor for genomic files - it compresses VCF/BCF, SAM/BAM, fastq, fasta, GVF and 23andMe files. If can even compress them if they are already compressed with .gz .bz2 .xz (for full list of supported file types see 'genozip --input --help').
It achieves x2 to x5 better compression ratios than gzip because it leverages some properties specific to genomic data to compress better. It is also a lot faster than gzip.
The compression is lossless - the decompressed file is 100% identical to the original file.
The command line options are similar to gzip and bcftools, so if you're familiar with these, it works pretty much the same. To get started, try: genozip --help
Commands: genozip - compress one or more files genounzip - decompress one or more files genols - show metadata of one or more files or the entire directory genocat - view one or more files
Some advanced options:
Lookups: genocat -r ^Y,MT file1.vcf -- displays all chromosomes except Y and MT genocat -r -10000 file1.vcf -- displays positions up to 10000 genocat -s SMPL1,SMPL2 file1.vcf -- displays 2 samples
Note: there is no need for a separate indexing step or index file
Even better compression, with some minor modifications of the data: genozipfile.vcf --optimize
Compress and then verify that the compressed file decompresses correctly: genozipfile.vcf --test
Do you find genozip to be helpful in your research? Please be so kind as to support continued development by citing
Citing:https://doi.org/10.1093/bioinformatics/btaa290
Feature requests and bug reports: bugs@genozip.com
genozip is free for non-commercial use. For a commercial license, please contact sales@genozip.com
Usage is subject to terms and conditions. The non-commercial license can be viewed with genozip --license
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.
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Compressor for genomic files (VCF/BCF, SAM/BAM, fastq, fasta, GVF, 23andMe), up to 5x better than gzip and faster too