So what is DeeZ?
DeeZ (a.k.a. DeeNA-Zip) is a tool for compressing SAM/BAM files, or more formally, a tool which does reference-based compression by local assembly. DeeZ was publised in Nature Methods in November 2014.
How do I get DeeZ?
Just clone our repository and issue
git clone https://github.com/sfu-compbio/deez.git cd dz && make -j
git clone https://bitbucket.org/compbio/dz.git git clone git://git.code.sf.net/p/deez-compression/deez deez-compression-deez
If you don’t have git, you can always fetch pre-packaged DeeZ archives:
Note: You will need at least g++ 4.4 to compile the sources.
How do I use DeeZ?
DeeZ is invoked as following:
deez -r [reference] [input.sam] -o [output]
This will compress
deez -r [reference] [input.dz] -o [output] ([region])
This will decompress
[region] is optional.
You can also specify the region of interest while decompressing (i.e. randomly access the region). For example, to extract some reads from chr16 to standard output, you should run:
deez -r [reference] input.dz -c chr16:15000000-16000000
Don’t forget to cite us if you use it in your research :)
--threads, -t [number]
Set up the number of threads DeeZ may use for compression and decompression.
Default value: 4
Outputs the SAM header.
--reference, -r [file|directory]
Specify the FASTA reference file.
Note: Chromosome names in the SAM and FASTA files must match. Also, instead of one big FASTA file, DeeZ supports reference lookup in the given directory for chr*.fa files, where chr* is the chromosome ID from the SAM file.
Force overwrite of exiting files.
Compress/decompress to the stdout.
--output, -o [file]
Compress/decompress to the
Set lossy parameter for quality lossy encoding (for more information, please check SCALCE).
--quality, -q [mode]
modeis 1 or samcomp, DeeZ will use sam_comp quality model to encode the qualities. Quality random access is not supported on those files.
--withflag, -f [flag]
Decompress only mappings which have
--withoutflag, -F [flag]
Decompress only mappings which do not have
Display mapping statistics (needs DeeZ file as input).
Sort the input SAM/BAM file by mapping location.
--sortmem, -M [size]
Maximum memory used for sorting.
Default value: 1G
Contact & Support
DeeZ has been brought to you by:
NSERC Discovery Grant
Vanier Canada Graduate Fellowships
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