readfish 0.0.4

Adaptive sampling toolkit for MinION

Installation

This toolkit currently requires MinKNOW (minknow-core v3.6) to be installed and read_until_api_v2 to be installed separately. We recommend installing in a virtual environment as so:

# Make a virtual env
python3 -m venv readfish
source ./readfish/bin/activate
pip install git+https://github.com/LooseLab/read_until_api_v2@master
pip install readfish

Usage

# 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