Compression

Genozip can run on any type of file, but it is optimized to compress genomic file formats.

Simple compression and decompression

genozip sample.bam

genounzip sample.bam.genozip

Compressing and decompressing FASTQ with paired-end reads with a reference

First, create a refrence file. This is a one-time step, that may take up to 10 minutes:
genozip --make-reference myfasta.fa

Second, compress or decompresses your file(s) using the reference:
genozip --reference myfasta.ref.genozip --pair mysample-R1.fastq.gz mysample-R2.fastq.gz

genounzip --reference myfasta.ref.genozip mysample-R1+2.fastq.genozip

Details

Compressing and decompressing multiple files into a tar file (preserving directory structure)

genozip *.bam --tar mysamples.tar

tar xvf mydata.tar | genounzip --files-from - --replace

Details

Using genozip in a pipline

genocat mysample.sam.genozip | samtools - .....

my-sam-outputing-method | genozip - --input sam --output mysample.sam.genozip

Viewing compression stats

genocat sample.bam.genozip --stats

Lookups, downsampling and other subsets

genocat --regions chr1:10000-20000 mysamples.vcf.genozip
Displays a specific region.

genocat --regions ^Y,MT mysample.bam.genozip
Displays all alignments except Y and MT contigs.

genocat --regions chrM GRCh38.fa.genozip
Dislays the sequence of chrM.

genocat --samples SMPL1,SMPL2 mysamples.vcf.genozip
Displays 2 samples.

genocat --grep 1101:2392 myreads.fq.genozip
Displays reads that have “1101:2392” anywhere in the description.

genocat --downsample 10 mysample.fq.genozip
Displays 1 in 10 reads.
Note: These are just some examples - there are many more subsetting options see genocat.

Compressing even better, with some minor modifications of the data

genozip file.bam --optimize
Note: compression with --optimize is not lossless - see genozip for details.

Compressing faster, sacrificing a bit of compression ratio

genozip file.bam --fast

Encrypting (256 bit AES)

genozip file.vcf --password abc
genounzip file.vcf.genozip --password abc

Details

Converting SAM/BAM to FASTQ

genounzip file.bam.genozip --fastq

Details
Generating a samtools/bcftools index file when uncompressing
genounzip file.bam.genozip --index

Calculating the MD5 of the underlying textual file (also included in –test)

genozip file.vcf --md5
genounzip file.vcf.genozip --md5
genols file.vcf.genozip

Compressing and then verifying that the compressed file decompresses correctly

genozip file.vcf --test