Welcome to the readfish documentation!

Citation

The paper is available at nature biotechnology and bioRxiv

If you use this software please cite: 10.1038/s41587-020-00746-x

Readfish enables targeted nanopore sequencing of gigabase-sized genomes Alexander Payne, Nadine Holmes, Thomas Clarke, Rory Munro, Bisrat Debebe, Matthew Loose Nat Biotechnol (2020); doi: https://doi.org/10.1038/s41587-020-00746-x

Other works

An update preprint is available at bioRxiv

Barcode aware adaptive sampling for Oxford Nanopore sequencers Alexander Payne, Rory Munro, Nadine Holmes, Christopher Moore, Matt Carlile, Matthew Loose bioRxiv (2021); doi: https://doi.org/10.1101/2021.12.01.470722

Installation

Our preferred installation method is via conda.

The environment is specified as:

name: readfish
channels:
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - python=3.10
  - pip
  - pip:
    - readfish[all]

Saving the snippet above as readfish_env.yml and running the following commands will create the environment.

conda env create -f readfish_env.yml
conda activate readfish

Apple Silicon

Some users may encounter an issue with grpcio on apple silicon. This can be fixed by reinstalling grpcio as follows:

pip uninstall grpcio
GRPC_PYTHON_LDFLAGS=" -framework CoreFoundation" pip install grpcio --no-binary :all:

Installing with development dependencies

A conda yaml file is available for installing with dev dependencies - development.yml

curl -LO https://raw.githubusercontent.com/LooseLab/readfish/e30f1fa8ac7a37bb39e9d8b49251426fe1674c98/docs/development.yml?token=GHSAT0AAAAAACBZL42IS3QVM4ZGPPW4SHB6ZE67V6Q
conda env create -f development.yml
conda activate readfish_dev

‼️ Important !!

MinKNOW has now transitioned from Guppy to Dorado. Until MinKNOW version 5.9 both Guppy and Dorado used ont-pyguppy-client-lib.
As of MinKNOW version 5.9 and Dorado server version 7.3.9 and greater Dorado required an alternate library, ont-pybasecall-client-lib, but guppy could still be used.
As of MinKNOW 6.0 Guppy support has been deprecated and only Dorado support is provided. It is important to ensure the correct library is installed for your specific configuration and the listed ont-pyguppy-client-lib or ont-pybasecaller-client-lib version may not match the versions installed on your system. To fix this, Please see this issue, using the appropriate library.

ONT’s Dorado Basecall Server GPU should be installed and running as a server.

Alternatively, install readfish into a python virtual-environment 
# Make a virtual environment
python3 -m venv readfish
. ./readfish/bin/activate
pip install --upgrade pip

# Install our readfish Software
pip install readfish[all]

# Install ont_pybasecall_client that matches your dorado basecall server version. E.G.
pip install ont_pybasecall_client_lib==7.1.2

Usage

 
usage: readfish [-h] [--version]  ...

positional arguments:
                   Sub-commands
    targets        Run targeted sequencing
    barcode-targets
                   Run targeted sequencing
    unblock-all    Unblock all reads
    validate       readfish TOML Validator

options:
  -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.

TOML File

For information on the readfish TOML files see TOML files

Acknowledgements

We’re really grateful to lots of people for help and support. Here’s a few of them…

From the lab: Teri Evans, Sam Holt, Lewis Gallagher, Chris Alder, Thomas Clarke

From ONT: Stu Reid, Chris Wright, Rosemary Dokos, Chris Seymour, Clive Brown, George Pimm, Jon Pugh

From the Nanopore World: Nick Loman, Josh Quick, John Tyson, Jared Simpson, Ewan Birney, Alexander Senf, Nick Goldman, Miten Jain, Lukas Weilguny

And for our Awesome Logo please checkout out @tim_bassford from @TurbineCreative!