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

Bioinformatics
Authors
Keywords
Abstract

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 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.

Availability and implementation: These tools are available as a part of the GATK at https://github.com/broadinstitute/gatk.

Supplementary information: Supplementary data are available at Bioinformatics online.

Year of Publication
2018
Journal
Bioinformatics
Volume
34
Issue
24
Pages
4287-4289
Date Published
2018 12 15
ISSN
1367-4811
DOI
10.1093/bioinformatics/bty501
PubMed ID
29982281
PubMed Central ID
PMC6289130
Links