Piper - A pipeline engine built on top of GATK Queue

What is Piper?

Piper is a workflow engine for handling data from next-generation sequencing experiments. It’s built on top of the GATK Queue framework, and started out at the SNP&SEQ Technology platform. It’s been put to large scale use in analyzing whole human genome sequencing data run at the National Genomics Infrastructure.

Piper builds on the concept of standardized workflows for different next-generation sequencing applications. At the moment Piper supports the following workflows:


For full documentation and instructions on how to use Piper see the README at Github.




See the code for Piper here: https://github.com/NationalGenomicsInfrastructure/piper/