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

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 configurabl...

Full description

Saved in:
Bibliographic Details
Published in:Bioinformatics Vol. 34; no. 24; pp. 4287 - 4289
Main Authors: Walker, Mark A, Pedamallu, Chandra Sekhar, Ojesina, Akinyemi I, Bullman, Susan, Sharpe, Ted, Whelan, Christopher W, Meyerson, Matthew
Format: Journal Article
Language:English
Published: England Oxford University Press 15.12.2018
Subjects:
Applications Notes
ISSN:1367-4803, 1367-4811, 1460-2059, 1367-4811
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
The authors wish it to be known that, in their opinion, the Mark A.Walker and Chandra Sekhar Pedamallu authors should be regarded as Joint First Authors.
ISSN:1367-4803
1367-4811
1460-2059
1367-4811
DOI:10.1093/bioinformatics/bty501