Pathogen-Host Analysis Tool (PHAT): an integrative platform to analyze next-generation sequencing data

Christopher M Gibb; Robert Jackson; Sabah Mohammed; Jinan Fiaidhi; Ingeborg Zehbe

doi:10.1093/bioinformatics/bty1003

Pathogen-Host Analysis Tool (PHAT): an integrative platform to analyze next-generation sequencing data

Bioinformatics. 2019 Aug 1;35(15):2665-2667. doi: 10.1093/bioinformatics/bty1003.

Authors

Christopher M Gibb^{1

2}, Robert Jackson^{1

3}, Sabah Mohammed², Jinan Fiaidhi², Ingeborg Zehbe^{1

4

5}

Affiliations

¹ Probe Development and Biomarker Exploration, Thunder Bay Regional Health Research Institute.
² Department of Computer Science, Lakehead University, Thunder Bay, Ontario, Canada.
³ Biotechnology Program, Lakehead University, Thunder Bay, Ontario, Canada.
⁴ Department of Biology, Lakehead University, Thunder Bay, Ontario, Canada.
⁵ Northern Ontario School of Medicine, Lakehead University, Thunder Bay, Ontario, Canada.

PMID: 30561651
DOI: 10.1093/bioinformatics/bty1003

Abstract

Summary: The Pathogen-Host Analysis Tool (PHAT) is an application for processing and analyzing next-generation sequencing (NGS) data as it relates to relationships between pathogens and their hosts. Unlike custom scripts and tedious pipeline programming, PHAT provides an integrative platform encompassing raw and aligned sequence and reference file input, quality control (QC) reporting, alignment and variant calling, linear and circular alignment viewing, and graphical and tabular output. This novel tool aims to be user-friendly for life scientists studying diverse pathogen-host relationships.

Availability and implementation: The project is available on GitHub (https://github.com/chgibb/PHAT) and includes convenient installers, as well as portable and source versions, for both Windows and Linux (Debian and RedHat). Up-to-date documentation for PHAT, including user guides and development notes, can be found at https://chgibb.github.io/PHATDocs/. We encourage users and developers to provide feedback (error reporting, suggestions and comments).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

High-Throughput Nucleotide Sequencing*
Quality Control
Software*