Pathogen-Host Analysis Tool (PHAT): an Integrative Platform to Analyze Pathogen-Host Relationships in Next-Generation Sequencing Data [article]

Christopher M. Gibb, Robert Jackson, Sabah Mohammed, Jinan Fiaidhi, Ingeborg Zehbe
2017 bioRxiv   pre-print
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 pathogen and host organisms. 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
more » ... novel tool aims to be user-friendly for life scientists studying diverse pathogen-host relationships. Availability and Implementation: The project is publicly available on GitHub ( 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 We encourage users and developers to provide feedback (error reporting, suggestions, and comments) using GitHub Issues.
doi:10.1101/178327 fatcat:6zibr36vjfdyvjihsxr77pepx4