Metadata-Version: 2.1
Name: readfish
Version: 0.0.5a2
Summary: Adaptive sampling toolkit for MinION
Home-page: https://github.com/LooseLab
Author: Alexander Payne
Author-email: alexander.payne@nottingham.ac.uk
License: UNKNOWN
Description: 
        Installation
        ---
        
        This toolkit currently requires MinKNOW (minknow-core v4.0.4) and Guppy (>=v4.0.11) 
        to be installed and [`read_until_api`](https://github.com/nanoporetech/read_until_api) 
        to be installed separately. We recommend installing in a virtual environment as so:
        
        ```bash
        # Make a virtual env
        python3 -m venv readfish
        source ./readfish/bin/activate
        pip install git+https://github.com/nanoporetech/read_until_api
        pip install --pre readfish
        ```
        
        Usage
        ---
        ```bash
        # check install
        $ readfish
        usage: readfish [-h] [--version]
                        {targets,align,centrifuge,unblock-all,validate,summary} ...
        
        positional arguments:
          {targets,align,centrifuge,unblock-all,validate,summary}
                                Sub-commands
            targets             Run targeted sequencing
            align               ReadFish and Run Until, using minimap2
            centrifuge          ReadFish and Run Until, using centrifuge
            unblock-all         Unblock all reads
            validate            ReadFish TOML Validator
            summary             Summary stats from FASTQ files
        
        optional arguments:
          -h, --help            show this help message and exit
          --version             show program's version number and exit
        
        See '<command> --help' to read about a specific sub-command.
        
        # example run command - change arguments as necessary:
        $ readfish targets --experiment-name "Test run" --device MN17073 --toml example.toml --log-file RU_log.log
        ```
        
Platform: UNKNOWN
Requires-Python: ==3.7
Description-Content-Type: text/markdown
