Usage: fastq-tools [OPTIONS] <COMMAND>

Commands:
  info          Show information about input
  grz-metadata  Show GRZ metadata
  scramble      Scramble input data
  help          Print this message or the help of the given subcommand(s)

Options:
  -i, --input <INPUT_FILE>  Input file
  -d, --decompress          Decompress input as gzip compressed data
  -h, --help                Print help
  -V, --version             Print version

Info

To show information about compressed FASTQ files use:

cat file_fastq.gz | gzip -d | fastq-tools info

To use build-in decompression of input data, use the --decompress/-d option:

cat file_fastq.gz | fastq-tools --decompress info

Using optional input file argument:

fastq-tools --decompress --input file_fastq.gz info

This will result in output like

GRZ Metadata

To generate GRZ metadata for a file use:

fastq-tools --decompress --input file_fastq.gz grz-metadata

The use of the --input argument is required for this sub command. If the file is an uncompressed FASTQ file, you can omit the --decompress option.

Supported file types are:

fastq (full support)
bam, bed, vcf (limited support)

Scramble

To scramble compressed FASTQ files use:

cat file_fastq.gz | gzip -d | fastq-tools scramble | gzip > scrambled_fastq.gz

This will scramble headers and sequences and write the output into scrambled_fastq.gz.

To use build-in decompression of input data, use the --decompress/-d option:

cat file_fastq.gz | fastq-tools -d scramble | gzip > scrambled_fastq.gz

Using optional input file argument:

fastq-tools -d -i file_fastq.gz scramble | gzip > scrambled_fastq.gz