Provides Python utilities to help with the management of sequencing data from Oxford Nanopore Technologies (ONT) instruments (specifically PromethION data) within the Bioinformatics Core Facility (BCF) at the University of Manchester.
It is recommended to install the code by first git cloning the
repository, and then using pip to install into a Python virtual
environment using pip, e.g.
$ git clone https://github.com/fls-bioinformatics-core/bcf_nanopore.git $ virtualenv -p python3 ./venv $ source ./venv/bin/activate $ pip install -r ./bcf_nanopore/requirements.txt $ pip install ./bcf_nanopore/
NB please use these instructions only as a starting point
The installed package can be configured via an .ini-style file
called bcf_nanopore.ini placed either in the current directory
or in the config directory of the package installation.
Note
A sample version of the config file called
bcf_nanopore.ini.sample can be found in the config
directory.
The package provides a single utility called bcf_nanopore which
in turn provides a set of subcommands.
To get general help run:
$ bcf_nanopore -h
The main commands are:
config: print current configuration informationinfo: reports information about a PromethION project directory containing outputs from one or more runs of the sequencersetup: creates an "analysis" directory for a PromethION projectfetch: copies a subset of data from the sequencer output for use with downstream analysisreport: reports the metadata from a PromethION project analysis directory
Documentation can be found here.
See CONTRIBUTING.md for guidelines on how to contribute to this project.