GATK PathSeq

GATK PathSeq identifies and characterizes microbial sequences in DNA and RNA short-read sequencing libraries from eukaryotic hosts, operating within the Genome Analysis Toolkit (GATK).

Key Features:

• Microbial Composition Reporting: Reports the microbial composition of DNA and RNA short-read sequencing samples, identifies known and unknown microbial sequences, and facilitates downstream assembly of novel organisms.
• Rapid Analysis: Performs sample analysis in a matter of minutes.
• Robust Parallelization: Built on the GATK engine and leveraging Apache Spark, PathSeq performs parallel read quality filtering, host subtraction, and microbial alignment across workstation, cluster, or cloud environments.
• Configurable Tools: Provides configurable tools within the GATK suite to tailor analysis parameters to specific experimental needs.

Scientific Applications:

• Microbiome profiling: Enables characterization of microbial diversity within eukaryotic hosts from sequencing libraries.
• Pathogen identification: Supports identification of pathogenic organisms in host-derived DNA and RNA sequencing data.
• Symbiosis studies: Facilitates exploration of symbiotic relationships between microbes and their eukaryotic hosts.
• Host–microbiome interaction: Enables investigation of the impact of microbial communities on host biology.
• Novel organism discovery: Supports assembly and discovery of previously uncharacterized microbial organisms from unknown sequences.

Methodology:

Applies read quality filtering, host sequence subtraction, and alignment of reads against known microbial databases.