Extract metrics from a fastq file, streaming. Output is a tab separated file containing
- read name
- read length
- average read quality
- median read quality
pip install fastqmetrics
fastqmetrics is written and tested on Python3, but could work on Python2.7.
fastqmetrics [-h] [-v] [-t THREADS] fastq positional arguments: fastq Fastq file to extract features from, can be compressed optional arguments: -h, --help Show this help message and exit -v, --version Print version and exit. -t, --threads THREADS Set the allowed number of threads to be used by the script.
fastqmetrics --threads 12 reads.fastq.gz > metrics.txt