Installation

amplimap is available through pip, so this command should install the pipeline as well as all required python packages.

#you may need to use `pip` instead of `pip3`
pip3 install amplimap

If this does not work, you can try to install it manually:

#install required python3 packages
#you may need to use `pip` instead of `pip3`
pip3 install setuptools Cython numpy

#download and install amplimap
#you may need to use `python` instead of `python3`
git clone --depth=1 https://github.com/koelling/amplimap.git
cd amplimap
python3 setup.py install

You can also download our requirements.txt file, which contains a full list of all Python packages used by amplimap, and a known working version.

Setup

To finish setting up amplimap you probably want to add the paths to the reference genome files you will be using (e.g. bwa index and reference genome fasta) to the Default configuration.

Requirements

• Linux environment (should also work on MacOS, Windows 10 Linux Subsystem)
• Python 3.5+ with setuptools, Cython and numpy
  • Further Python dependencies are listed in requirements.txt but can also be installed automatically by setup.py
• Reference genome FASTA file, with indices
• Required software:
  • At least one read aligner: BWA (tested with v0.7.12), Bowtie2 (tested with v2.2.5), STAR (tested with v2.5.1b)
  • bedtools (tested with v2.27.1)
  • samtools (tested with v1.5)
• Additional software for germline variant calling (optional):
  • At least one variant caller: Platypus 0.8.1+, GATK 4+
  • Annovar (tested with v2015-06-17)
  • bcftools (tested with v1.5)
• Additional software for low-frequency variant calling (optional):
  • Mutect2 (from GATK 4, tested with v4.0)
• Additional software for capture probe processing (optional):
  • Picard Tools 2+ (tested with v2.3.0)

If you do not have these required tools available yet, see Extended installation guide for amplimap for details on how to install them.