https://github.com/divonlan/genozip

A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too
https://github.com/divonlan/genozip

23andme bam bgzip bwa compression cram fasta fastq genomics gvf gzip sam samtools vcf

Last synced: 3 months ago
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A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too

• Host: GitHub
• URL: https://github.com/divonlan/genozip
• Owner: divonlan
• License: other
• Created: 2019-12-15T05:23:54.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2024-05-28T21:11:39.000Z (5 months ago)
• Last Synced: 2024-06-08T08:52:02.152Z (5 months ago)
• Topics: 23andme, bam, bgzip, bwa, compression, cram, fasta, fastq, genomics, gvf, gzip, sam, samtools, vcf
• Language: C
• Homepage:
• Size: 979 MB
• Stars: 149
• Watchers: 1
• Forks: 11
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

Awesome Lists containing this project

• Awesome-Bioinformatics - Genozip - A compressor of common genomic file formats (BAM, CRAM, FASTQ, VCF etc). [ [web](https://genozip.com/?utm_source=Awesome-Bioinformatics) | [paper-2021](https://www.researchgate.net/publication/349347156_Genozip_-_A_Universal_Extensible_Genomic_Data_Compressor) ] (Data Tools / Compressing)

README

        


[![Current Release](https://img.shields.io/github/v/release/divonlan/genozip "Current Release")](https://github.com/divonlan/genozip/releases/latest) [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/genozip?label=Conda%20Downloads&style=flat-square)](https://anaconda.org/conda-forge/genozip)

Genozip






Genozip is a lossless compressor for  FASTQ, BAM/CRAM, VCF and many other genomic files - see https://genozip.com





Genozip is also available on Conda and binary downloads, see installation options.





Building from source: make -j (required for building: gcc 8.5 or above ; nasm).





New: Genozip 15 - with Deep™ - losslessly co-compressing BAM and FASTQ files:


![v15 deep benchmark](https://github.com/divonlan/genozip/assets/56345591/39c7e9c5-135d-49c9-9213-89d4b830842a)

Genozip Genozip is a commercial product, but we make it free for certain academic research use. See eligibility and other licensing options or contact [email protected] 





IMPORTANT: Genozip is a commercial product, NOT AN OPEN SOURCE product - we provide our source code to assure users that they will always have access to the code needed to decompress their files. HOWEVER, reverse engineering, code modifications, derivative works or inclusion of the code or parts thereof into other software packages is strictly forbidden by the license.





Attributions for 3rd party source components: attributions.





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 AUTHORS, COPYRIGHT HOLDERS OR DISTRIBUTORS OF THIS SOFTWARE BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.