pangraph
a bioinformatic toolkit to align large sets of genome assemblies into a graph data structure
install requirements
- python >= 3.8
- pipenv
- mash
- minimap2
- GNUmake (optional for build)
manual
run pipenv sync to pull all dependencies into a virtual environment
run ./bin/setup_pangraph to download mash && minimap2 binaries [optional-linux only]
append ./bin to your system path
build
the repo contains a Makefile that will generate and analyze synthetic data.
the input is the targets file, each simulation run is given by a line entry.
the synthetic data can be generated (e.g. with 4 cores) by running make -j4