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

By David Arndt, Jason R. Grant, A. Marcu, Tanvir Sajed, Allison Pon, Yongjie Liang, David S. Wishart. Nucleic Acids Res., 2016

3,200 citations recorded by the source corpus.

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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c008e7ac3a0a09e10fc9bca1f62d7f09c4391400

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Citations in the corpus

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data (2017, background): “Additionally, most of these prophage predictors are not optimized to process large numbers of contigs in a reasonable time (see [13]), the exception being PHASTER, an updated version of PHAST [14].”
Identifying viruses from metagenomic data using deep learning (2020, methodology): “Before the metagenomic era, several tools for identifying proviruses from within prokaryotic genomes were developed [14 – 17].”
VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences (2020, methodology): “Other tools, predominantly PHASTER [47] and Prophage Hunter [48], are specialized in identifying integrated proviruses from whole genomes rather than scaffolds generated by metagenomic assemblies.”