1.0.0

Initial Release

This repo contains workflows for computational pathogen discovery using PathSeq, a pipeline in the Genome Analysis Toolkit (GATK) for detecting microbial organisms in short-read deep sequencing samples taken from a host organism.

Additional Resources:

• How to Run the Pathseq pipeline (manually)
• GATK PathSeq: a customizable computational tool for the discovery and identification of microbial sequences in libraries from eukaryotic hosts