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Bioinformatics DOI:10.1093/bioinformatics/bty501

GATK PathSeq: A customizable computational tool for the discovery and identification of microbial sequences in libraries from eukaryotic hosts.

Publication TypeJournal Article
Year of Publication2018
AuthorsWalker, MA, Pedamallu, CSekhar, Ojesina, AI, Bullman, S, Sharpe, T, Whelan, CW, Meyerson, M
Date Published2018 Jul 04

Summary: We present an updated version of our computational pipeline, PathSeq, for the discovery and identification of microbial sequences in genomic and transcriptomic libraries from eukaroyotic hosts. This pipeline is available in the Genome Analysis Toolkit (GATK) as a suite of configurable tools that can report the microbial composition of DNA or RNA short-read sequencing samples and identify unknown sequences for downstream assembly of novel organisms. GATK PathSeq enables sample analysis in minutes at low cost. In addition, these tools are built with the GATK engine and Apache Spark framework, providing robust, rapid parallelization of read quality filtering, host subtraction, and microbial alignment in workstation, cluster, and cloud environments.

Availability: These tools are available as a part of the GATK at

Supplementary information: Supplementary data are available at Bioinformatics online. Detailed descriptions of the PathSeq tools, introductory tutorial, and a resource bundle of pre-built references are available at and


Alternate JournalBioinformatics
PubMed ID29982281