# FASTQ tools Application to show information about and scramble FASTQ files to provide non-sensitive data for development purposes ## Usage This application provides the following subcommands ``` Usage: fastq-tools [OPTIONS] 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 -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: ```shell cat file_fastq.gz | gzip -d | fastq-tools info ``` To use build-in decompression of input data, use the `--decompress`/`-d` option: ```shell cat file_fastq.gz | fastq-tools --decompress info ``` Using optional input file argument: ```shell fastq-tools --decompress --input file_fastq.gz info ``` This will result in output like ![Info subcommand](docs/info_subcommand.jpg) ### GRZ Metadata To generate GRZ metadata for a file use: ```shell 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. ![GRZ Metadata subcommand](docs/grz-metadata_subcommand.jpg) Supported file types are: * fastq (full support) * bam, bed, vcf (limited support) ### Scramble To scramble compressed FASTQ files use: ```shell 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: ```shell cat file_fastq.gz | fastq-tools -d scramble | gzip > scrambled_fastq.gz ``` Using optional input file argument: ```shell fastq-tools -d -i file_fastq.gz scramble | gzip > scrambled_fastq.gz ```