Table of contents

TAPAS (Testing Aligner Performance for Ancient Samples) is a software package written in Python and R which enables you to test how well parameters of NGS short read mappers perform when mapping reads to a reference. The reads can be subjected to artificial damage to simulate evolutionary distance and chemical alteration of ancient DNA samples.


Download the package from the project's GitHub page

See the section Dependencies of the scripts to learn about the installation process of TAPAS


TAPAS can be used to generate artificial NGS reads from a given reference genome, introduce mutations into them which follow a user-defined pattern and evaluate the mapping success of the reads with a user-supplied short read mapper.

See the section about Input files to see which files must be supplied prior to the analysis.

In the following, the workflow is outlined, where links are provided to manual chapters which give more detail on each step.

Apart from that, the Appendix lists additional information: