Quick Start - Genetalks/gtz GitHub Wiki

GTX.Zip Professional needs to be installed on the current machine. If not, please see Installation Guide .

Take the human sample species as an example, make the index file (bin file) required for GTX.Zip high rate compression

• Download the 1th rbin file ("1" is the number of the human rbin file in the gtx_index list) and gtz_index will save it to the default path (~/.config/gtz):

  gtz_index download 1

  or

  You can download rbin file from here ( Homo_sapiens rbin file )

• Make the bin file ( may need 100GB free disk space, and >28GB memory, and 10 mins)

  gtz_index makeindex ~/.config/gtz/Homo_sapiens_bcacac9064331276504f27c6cf40e580.rbin

  * bin file：The index file used for hight compression.The default file path is："~/.config/gtz/"
  * rbin file：The compact index file used for decompression.The default file path is："~/.config/gtz/"

gtz sample.fq -o sample.fq.gtz --bin-file ~/.config/gtz/Homo_sapiens_bcacac9064331276504f27c6cf40e580.bin

sample.fq can be downloaded from https://gtz.io/sample.fq. (2GB fastq file, extracted from a real WES data produced by Novaseq)

*gtz can also directly compress fastq.gz file.