Metadata-Version: 2.1
Name: pyfastq_filter
Version: 0.4.2
Summary: filters FASTQ files
Home-page: https://github.com/ahcm/pyfastq_filter
Author: Andy Hauser
Author-email: Andreas.Hauser@LMU.de
License: LICENSE
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
License-File: LICENSE

# pyfastq_filter

Filter FASTQ Files.

# Installation

```bash
pip3 install --user pyfastq_filter
```

# Usage

```
Usage:
  pyfastq_filter.py [-q i] [-l n] [-m m] [-o OUTNAME] FASTQ

Options:
  -l --length=n      minimum length to let through [default: 300]
  -m --max-length=m  maximum length to let through [default: infinity]
  -q --quality=i     minimum quality to let through [default: 10]
  -o --outfile=FILE  output filename, otherwise STDOUT [default: -]
```


Extract only FASTQ entries with sequence length >= 5000 and mean quality >= 12:

```bash
pyfastq_filter.py -q 12 -l 5000 example.fastq > example-q12-l5000.fastq
```
