PHASTER: a better, faster version of the PHAST phage search tool

TLDR

PHASTER is an enhanced version of the PHAST web server that rapidly identifies and annotates prophage sequences in bacterial genomes and plasmids. It preserves the PHAST pipeline while incorporating software optimizations, hardware upgrades, a rewritten web interface, a new graphical genome browser, automated database pruning, improved multi‑query handling, and rapid look‑ups against 14,000 pre‑annotated genomes. These improvements make PHASTER 4.3× faster than PHAST, with a backend 2.7× speed‑up and 80 additional CPUs, enabling a typical genome to be processed in 3 min from raw sequence or 1.5 min from a GenBank file, and allowing complete annotations in seconds for pre‑annotated genomes, and it is available at www.phaster.ca.

Abstract

PHASTER (PHAge Search Tool – Enhanced Release) is a significant upgrade to the popular PHAST web server for the rapid identification and annotation of prophage sequences within bacterial genomes and plasmids. Although the steps in the phage identification pipeline in PHASTER remain largely the same as in the original PHAST, numerous software improvements and significant hardware enhancements have now made PHASTER faster, more efficient, more visually appealing and much more user friendly. In particular, PHASTER is now 4.3× faster than PHAST when analyzing a typical bacterial genome. More specifically, software optimizations have made the backend of PHASTER 2.7X faster than PHAST, while the addition of 80 CPUs to the PHASTER compute cluster are responsible for the remaining speed-up. PHASTER can now process a typical bacterial genome in 3 min from the raw sequence alone, or in 1.5 min when given a pre-annotated GenBank file. A number of other optimizations have also been implemented, including automated algorithms to reduce the size and redundancy of PHASTER's databases, improvements in handling multiple (metagenomic) queries and higher user traffic, along with the ability to perform automated look-ups against 14 000 previously PHAST/PHASTER annotated bacterial genomes (which can lead to complete phage annotations in seconds as opposed to minutes). PHASTER's web interface has also been entirely rewritten. A new graphical genome browser has been added, gene/genome visualization tools have been improved, and the graphical interface is now more modern, robust and user-friendly. PHASTER is available online at www.phaster.ca.