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! |
|---|
The listed |
ONT’s Guppy 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_pyguppy_client_lib that matches your guppy server version. E.G.
pip install ont_pyguppy_client_lib==6.3.8
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!