Q100bench

Q100bench is a software package for reporting differences between an assembly or read dataset and a benchmark assembly, such as the Q100 assembly of the sample HG002.

Install

Software dependencies

Q100bench requires bedtools (https://bedtools.readthedocs.io/en/latest/), and R with Bioconductor (https://www.bioconductor.org/).

Until q100bench is available on PyPi and bioconda, the easiest way to use it is to install it locally. First clone this github repository:

git clone https://github.com/nhansen/q100bench.git
cd q100bench

Create a virtual environment for the project:

python3 -m venv venv
source venv/bin/activate

Finally use python’s pip installer to install and test a development copy for yourself to run:

python3 -m pip install -e .
pytest