Pomoxis - bioinformatics tools for nanopore research¶
© 2018 Oxford Nanopore Technologies Ltd.
Pomoxis comprises a set of basic bioinformatic tools tailored to nanopore sequencing. Notably tools are included for generating and analysing draft assemblies. Many of these tools are used by the research data analysis group at Oxford Nanopore Technologies.
See Pomoxis Examples for common simple tasks.
- Wraps third party tools with known good default parameters and methods of use.
- Creates an isolated environment with all third-party tools.
- Can be installed with conda.
- Streamlines common short analysis chains.
- Includes a nanopore read simulator.
- Server/client components for minimap2 and bwa.
- Integrates into katuali for performing more complex analysis pipelines.
- Open source (Mozilla Public License 2.0).
Research releases are provided as technology demonstrators to provide early access to features or stimulate Community development of tools. Support for this software will be minimal and is only provided directly by the developers. Feature requests, improvements, and discussions are welcome and can be implemented by forking and pull requests. However much as we would like to rectify every issue and piece of feedback users may have, the developers may have limited resource for support of this software. Research releases may be unstable and subject to rapid iteration by Oxford Nanopore Technologies.
Pomoxis is developed on Ubuntu 16.04, other recent linuxes should be equally compatible (see build notes below). Pomoxis is known to work on at least some MacOS High Sierra configurations, though some components, notably scrappy, are known to not work on some MacOS configurations (combinations of OS and xcode versions).
Much of pomoxis’s functionality is dependent on thirty party tools. These can be provided by the user, or can be installed with the help of the provided Makefile
Installation with conda
Pomoxis can be installed using the conda package manager. Many users will prefer this method. If make is installed on the system, the following will create a conda environment and install pomoxis and its third party dependencies into the environment:
git clone --recursive https://github.com/nanoporetech/pomoxis cd pomoxis CONDA=<path to conda install> make conda
On the final line, use for example:
CONDA=~/miniconda3/ make conda
A conda package is planned in the future.
Installation with pip
Pomoxis can be installed using the python package manager, pip:
pip install git+https://github.com/rrwick/Porechop pip install pomoxis
We recommend using medaka within a virtual environment, viz.:
virtualenv pomoxis --python=python3 --prompt "(pomoxis) " . pomoxis/bin/activate pip install git+https://github.com/rrwick/Porechop pip install pomoxis
Using this method requires the user to provide several binaries:
and place these within the PATH.
Installation from source
With this method pomoxis will install itself into a an isolated virtual environment. The installation will fetch, compile, and install all direct dependencies into the environment. Use this method if you do not wish to use conda, but will not be providing the third-party binaries.
Before installing pomoxis is may be required to install some prerequisite packages, best installed by a package manager. On Ubuntu these are:
gcc-4.9 g++-4.9 zlib1g-dev libncurses5-dev python3-all-dev libhdf5-dev libatlas-base-dev libopenblas-base libopenblas-dev libbz2-dev liblzma-dev libffi-dev make python-virtualenv cmake wget bzip2
To setup the environment run:
git clone --recursive https://github.com/nanoporetech/pomoxis cd pomoxis make install . ./venv/bin/activate
The installation of porechop (https://github.com/rrwick/Porechop) requires a newer compiler than is a available on some systems. It may therefore be necessary to install a newer compiler and set environment variables before the make install step:
# For porechop to be compiled on older systems set these, e.g.: export CXX="g++-4.9" CC="gcc-4.9"
Note also that racon requires at least gcc>=4.8.5 to [compile smoothly](https://github.com/isovic/racon/issues/57).
Installation without compiling third-party binaries
Running the above within a pre-exisiting (virtual) environnment may well fail; advanced may wish to simply run
python setup.py install
in the standard manner after compiling the third party programs listed below and ensuring they are present on the PATH. The setup.py script can copy the binaries into the python interpreter path if they are placed within a directory named bincache alongside setup.py. To make use of this facility run:
pip install -r requirements.txt POMO_BINARIES=1 python setup.py install
Third party binaries¶
The distribution bundles some common bioinformatics tools: