Metadata-Version: 1.0
Name: fqutil
Version: 1.1
Summary: Several useful tools for manipulating FASTQ files.
Home-page: https://github.com/jstaf/fqutil
Author: Jeff Stafford
Author-email: jeff.stafford@queensu.ca
License: BSD-3
Description-Content-Type: text/markdown
Description: # fqutils
        
        A couple Python-based FASTQ QC tools that perform several useful file handling operations, 
        notably check read-pairing, repair read-pairing, and trim reads. 
        Notably, `fq-repair` is the only tool (to my knowledge) 
        that can successfully re-pair reads from gzipped FASTQ input.
        All tools are designed to be as fast and memory-efficient as possible.
        Input is assumed to be 4-line FASTQ and may be gzipped.
        
        ## Installation and tests
        
        `fqutils` has no dependencies aside from the Python 3 standard library 
        (if this Python is installed, things will work).
        Just clone the repository with with `git clone https://github.com/jstaf/fqutils.git`.
        Clever users will also note that this repository can be installed as a python package with `pip install .`  
        
        To run tests: `pytest`
        
        ## Current scripts
        
        Run `commandname --help` for individual usage instructions.
        Sample commands can also be found in the `tests/` directory.
        
        * **fq-checkpair** - Check if two FASTQ files are properly paired and highlight errors.
        
        * **fq-trim** - Starting from both ends, trim a read so that bases below a certain Phred quality score are removed. Resulting reads shorter than a minimum length are removed. Fast, dirty, and idiot-proof trimming.
        
        * **fq-repair** - Re-pair the reads in two FASTQ files if reads have been filtered out or otherwise reordered. 
        
        * **fq-zwc** - Just a wrapper around `wc -l` for gzipped files.
        
Platform: UNKNOWN
