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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 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.

SUBMITTER: Walker MA

PROVIDER: S-EPMC6289130 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature

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

Walker Mark A MA Pedamallu Chandra Sekhar CS Ojesina Akinyemi I AI Bullman Susan S Sharpe Ted T Whelan Christopher W CW Meyerson Matthew M

Bioinformatics (Oxford, England) 20181201 24

<h4>Summary</h4>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 anal ...[more]

PMID: 29982281

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Project description:Protists have traditionally been identified by cultivation and classified taxonomically based on their cellular morphologies and behavior. In the past decade, however, many novel protist taxa have been identified using cultivation independent ssu rRNA sequence surveys. New rRNA "phylotypes" from uncultivated eukaryotes have no connection to the wealth of prior morphological descriptions of protists. To link phylogenetically informative sequences with taxonomically informative morphological descriptions, we demonstrate several methods for combining whole cell rRNA-targeted fluorescent in situ hybridization (FISH) with cytoskeletal or organellar immunostaining. Either eukaryote or ciliate-specific ssu rRNA probes were combined with an anti-α-tubulin antibody or phalloidin, a common actin stain, to define cytoskeletal features of uncultivated protists in several environmental samples. The eukaryote ssu rRNA probe was also combined with Mitotracker® or a hydrogenosomal-specific anti-Hsp70 antibody to localize mitochondria and hydrogenosomes, respectively, in uncultivated protists from different environments. Using rRNA probes in combination with immunostaining, we linked ssu rRNA phylotypes with microtubule structure to describe flagellate and ciliate morphology in three diverse environments, and linked Naegleria spp. to their amoeboid morphology using actin staining in hay infusion samples. We also linked uncultivated ciliates to morphologically similar Colpoda-like ciliates using tubulin immunostaining with a ciliate-specific rRNA probe. Combining rRNA-targeted FISH with cytoskeletal immunostaining or stains targeting specific organelles provides a fast, efficient, high throughput method for linking genetic sequences with morphological features in uncultivated protists. When linked to phylotype, morphological descriptions of protists can both complement and vet the increasing number of sequences from uncultivated protists, including those of novel lineages, identified in diverse environments.

Dataset Information

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

Publications

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

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