fastq-anonymous

Change the sequence and identifier of a fastq file to enable sharing of confidential information for troubleshooting

INSTALLATION

pip install fastq-anonymous

USAGE

Reads from stdin and writes to stdout. Sequences are by default replaced by random nucleotides.
Fastq identifiers and description are also anonymized.
Read lengths and quality strings are preserverd.

optional arguments:
  -h, --help     show this help message and exit
  -v, --version  Print version and exit.
  -m, --mask     Mask all nucleotides using N

EXAMPLES

cat reads.fastq.gz | fastq-anonymous > anonymous_reads.fastq

gunzip -c reads.fastq.gz | fastq-anonymous > anonymous_reads.fastq

gunzip -c reads.fastq.gz | fastq-anonymous | gzip > anonymous_reads.fastq.gz