• python 3.4 and higher

  • unix sort

  • bgzip

  • pbgzip (optional)

  • samtools >= 1.4

  • Python packages Cython, numpy, click, nose

We highly recommend using the conda package manager to install scientific packages and their dependencies. To get conda, you can download either the full Anaconda Python distribution which comes with lots of data science software or the minimal Miniconda distribution which is just the standalone package manager plus Python. In the latter case, you can install the packages as follows:

$ conda install samtools sort bgzip pbgzip Cython numpy pip
$ pip install click nose

Install the latest version of pairsamtools using pip.

$ pip install git+https://github.com/mirnylab/pairsamtools