gatk4-pathseq

Purpose :

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

pathseq-pipeline

Runs the PathSeq pipeline

Requirements/expectations :

• BAM
  • File must pass validation by ValidateSamFile
  • All reads must have an RG tag
  • One or more read groups all belong to a single sample (SM)
• Host and microbe references files available in the GATK Resource Bundle

Output :

• BAM file containing microbe-mapped reads and reads of unknown sequence
• Tab-separated value (.tsv) file of taxonomic abundance scores
• Picard-style metrics files for the filter and scoring phases of the pipeline

pathseq-build-microbe-reference

Builds a microbe reference for use with PathSeq

Requirements/expectations :

• FASTA file containing microbe sequences from NCBI RefSeq

Output :

• FASTA index and dictionary files
• GATK BWA-MEM index image
• PathSeq taxonomy file

pathseq-build-host-reference

Builds a host reference for use with PathSeq

Requirements/expectations :

• FASTA file containing host sequences

Output :

• FASTA index and dictionary files
• GATK BWA-MEM index image
• PathSeq Kmer file

---

Software version notes

• GATK 4 or later
• Cromwell version support
  • Successfully tested on v36
  • Does not work on versions < v23 due to output syntax

Important Notes :

• Runtime parameters are optimized for Broad's Google Cloud Platform implementation.
• The provided JSON is a ready to use example JSON template of the workflow. Users are responsible for reviewing the GATK Tool and Tutorial Documentations to properly set the reference and resource variables.
• For help running workflows on the Google Cloud Platform or locally please view the following tutorial (How to) Execute Workflows from the gatk-workflows Git Organization.
• Please visit the User Guide site for further documentation on our workflows and tools.
• Relevant reference and resources bundles can be accessed in Resource Bundle.

Contact Us :

• The following material is provided by the Data Science Platforum group at the Broad Institute. Please direct any questions or concerns to one of our forum sites : GATK or Terra.

LICENSING

Copyright Broad Institute, 2018 | BSD-3

This script is released under the WDL source code license (BSD-3) (see LICENSE in https://github.com/broadinstitute/wdl). Note however that the programs it calls may be subject to different licenses. Users are responsible for checking that they are authorized to run all programs before running this script.