fastqmetrics
Extract metrics from a fastq file, streaming. Output is a tab separated file containing
- read name
- read length
- average read quality
- median read quality
INSTALLATION
pip install fastqmetrics
fastqmetrics is written and tested on Python3, but could work on Python2.7.
USAGE
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.
Example usage
fastqmetrics --threads 12 reads.fastq.gz > metrics.txt