Hardware-Accelerated Compression and Decompression
Gzip compression is ubiquitous in bioinformatics. FASTQ files are often gzipped, and the BAM format itself is a specialized version of gzip. For that reason, the DRAGEN BioIT processor provides hardware support for accelerating compression and decompression of gzipped data. If your input files are gzipped, DRAGEN detects that and decompresses the files automatically. If your output is BAM files, then the files are automatically compressed.
DRAGEN provides standalone command-line utilities to enable you to compress or decompress arbitrary files. These utilities are analogous to the Linux gzip and gunzip commands, but are named dzip and dunzip (dragen zip and dragen unzip). Both utilities are able to accept as input a single file, and produce a single output file with the .gz file extension removed or added, as appropriate. For example:
dzip file1 # produces output file file1.gz
dunzip file2.gz # produces output file file2
Currently, dzip and dunzip have the following limitations and differences from gzip/gunzip:
| • | Each invocation of these tools can handle only a single file. Additional file names (including those produced by a wildcard * character) are ignored. |
| • | They cannot be run at the same time as the DRAGEN host software. |
| • | They do not support the command line options found in gzip and gunzip (eg, --recursive, --fast, ‑‑best, ‑‑stdout). |