Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform

Abstract

BackgroundThe detection of pathogens in complex sample backgrounds has been revolutionized by wide access to next-generation sequencing (NGS) platforms. However, analytical methods to support NGS platforms are not as uniformly available. Pathosphere (found at Pathosphere.org) is a cloud - based open - sourced community tool that allows for communication, collaboration and sharing of NGS analytical tools and data amongst scientists working in academia, industry and government. The architecture allows for users to upload data and run available bioinformatics pipelines without the need for onsite processing hardware or technical support.ResultsThe pathogen detection capabilities hosted on Pathosphere were tested by analyzing pathogen-containing samples sequenced by NGS with both spiked human samples as well as human and zoonotic host backgrounds. Pathosphere analytical pipelines developed by Edgewood Chemical Biological Center (ECBC) identified spiked pathogens within a common sample analyzed by 454, Ion Torrent, and Illumina sequencing platforms. ECBC pipelines also correctly identified pathogens in human samples containing arenavirus in addition to animal samples containing flavivirus and coronavirus. These analytical methods were limited in the detection of sequences with limited homology to previous annotations within NCBI databases, such as parvovirus. Utilizing the pipeline-hosting adaptability of Pathosphere, the analytical suite was supplemented by analytical pipelines designed by the United States Army Medical Research Insititute of Infectious Diseases and Walter Reed Army Institute of Research (USAMRIID-WRAIR). These pipelines were implemented and detected parvovirus sequence in the sample that the ECBC iterative analysis previously failed to identify.ConclusionsBy accurately detecting pathogens in a variety of samples, this work demonstrates the utility of Pathosphere and provides a platform for utilizing, modifying and creating pipelines for a variety of NGS technologies developed to detect pathogens in complex sample backgrounds. These results serve as an exhibition for the existing pipelines and web-based interface of Pathosphere as well as the plug-in adaptability that allows for integration of newer NGS analytical software as it becomes available.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0840-5) contains supplementary material, which is available to authorized users.

Targeted Sequencing of Respiratory Viruses in Clinical Specimens for Pathogen Identification and Genome-Wide Analysis

“…Sequence the lib pool with PhiX control using Illumina MiSeq or NextSeq system. The acquired sequence data can be applied to bioinformatics data analysis pipeline, which may include data quality processing, the removal of human genome and transcriptome sequences, de novo assembly, and comparison of sequence contigs and unassembled reads with sequence databases using BLAST programs [12] (see Note 12).…”

Introduction of a Bayesian Network Builder Algorithm - Personalized Infectious Disease Risk Prediction

“…A support for more complex pathogen model (Kilianski, et al, 2015) (Huang, et al, 2012) would be beneficial.…”

Relating next-generation sequencing and bioinformatics concepts to routine microbiological testing

“…Its analytical capabilities include taxonomic analysis of sequence files, sequence assembly, and pathogen identification using a variety of databases, including NCBI. The software allows automating the work, being only necessary to upload the FASTQ files (or other formats) in the user interface, then select the identification pipeline and, finally, wait for the report generation (61).…”