Pomoxis contains a set of services to perform analysis of squiggles as they are produced in real-time along with fast pipelines for generating draft assemblies.
Documentation can be found at https://nanoporetech.github.io/pomoxis/.
Currently pomoxis supports only unix-like environments.
Pomoxis should be installed inside a virtual environment. A Makefile is provided to create a fresh environment, and to fetch, compile and install all direct dependencies into the environment.
To setup the environment run:
git clone --recursive https://github.com/nanoporetech/pomoxis
cd pomoxis
# For porechop to be compiled on older systems set these, e.g.:
# export CXX="g++-4.9" CC="gcc-4.9"
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 variables as in the above.
Running the above within a pre-exisiting virtual environnment may well fail;
advanced may wish to simply run the setup.py file in the standard manner
after compiling the third party programs as in the Makefile.
The distribution bundles some common bioinformatics tools (some of which are not currently used by pomoxis itself):
- miniasm
- minimap (to be deprecated)
- minimap2
- racon
- bwa
- samtools
- porechop
These will be compiled and installed into the virtual environment created as above.