GATK PathSeq: a customizable computational tool for the discovery and identification of microbial sequences in libraries from eukaryotic hosts | Zendy

Mark Walker | Zendy; Chandra Sekhar Pedamallu | Zendy; Akinyemi I. Ojesina | Zendy; Susan Bullman | Zendy; Ted Sharpe | Zendy; Christopher W. Whelan | Zendy; Matthew Meyerson | Zendy

Open Access

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

Author(s) -

Mark Walker,

Chandra Sekhar Pedamallu,

Akinyemi I. Ojesina,

Susan Bullman,

Ted Sharpe,

Christopher W. Whelan,

Matthew Meyerson

Publication year - 2018

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bty501

Subject(s) - identification (biology) , computational biology , computer science , biology , ecology

We present an updated version of our computational pipeline, PathSeq, for the discovery and identification of microbial sequences in genomic and transcriptomic libraries from eukaryotic 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.

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