fastqmetrics

Het hoeft voor


Keywords
nanopore, sequencing, processing
License
MIT
Install
pip install fastqmetrics==0.1.0

Documentation

fastqmetrics

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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