multiPhATE: bioinformatics pipeline for functional annotation of phage isolates

Ecale Zhou, Carol L.; Malfatti, Stephanie; Kimbrel, Jeffrey; Philipson, Casandra; McNair, Katelyn; Hamilton, Theron; Edwards, Robert; Souza, Brian

doi:10.1093/bioinformatics/btz258

multiPhATE: bioinformatics pipeline for functional annotation of phage isolates

Journal Article · Tue May 14 00:00:00 EDT 2019 · Bioinformatics

DOI:https://doi.org/10.1093/bioinformatics/btz258· OSTI ID:1602659

Ecale Zhou, Carol L. ^[1]; Malfatti, Stephanie ^[1]; Kimbrel, Jeffrey ^[1]; Philipson, Casandra ^[2]; McNair, Katelyn ^[3]; Hamilton, Theron ^[4]; Edwards, Robert ^[3]; Souza, Brian ^[1]

Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Naval Medical Research Center, Fort Detrick, MD (United States); San Diego State Univ., CA (United States)
San Diego State Univ., CA (United States)
Naval Medical Research Center, Fort Detrick, MD (United States)

To address the need for improved phage annotation tools that scale, we created an automated throughput annotation pipeline: multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is a throughput pipeline driver that invokes an annotation pipeline (PhATE) across a user-specified set of phage genomes. This tool incorporates a de novo phage gene calling algorithm and assigns putative functions to gene calls using protein-, virus- and phage-centric databases. multiPhATE’s modular construction allows the user to implement all or any portion of the analyses by acquiring local instances of the desired databases and specifying the desired analyses in a configuration file. We demonstrate multiPhATE by annotating two newly sequenced Yersinia pestis phage genomes. Within multiPhATE, the PhATE processing pipeline can be readily implemented across multiple processors, making it adaptable for throughput sequencing projects. Software documentation assists the user in configuring the system.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA)

Grant/Contract Number:: AC52-07NA27344

OSTI ID:: 1602659

Report Number(s):: LLNL-JRNL--757832; 943841

Journal Information:: Bioinformatics, Journal Name: Bioinformatics Journal Issue: 21 Vol. 35; ISSN 1367-4803

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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