multiPhATE: bioinformatics pipeline for functional annotation of phage isolates

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

doi:10.1093/bioinformatics/btz258

multiPhATE: bioinformatics pipeline for functional annotation of phage isolates

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

Research output: Contribution to journal › Article › peer-review

26 Citations (Scopus)

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Abstract

Summary: 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. Availability and implementation: multiPhATE was implemented in Python 3.7, and runs as a command-line code under Linux or Unix. multiPhATE is freely available under an open-source BSD3 license from https://github.com/carolzhou/multiPhATE. Instructions for acquiring the databases and third-party codes used by multiPhATE are included in the distribution README file. Users may report bugs by submitting to the github issues page associated with the multiPhATE distribution. Supplementary information: Supplementary data are available at Bioinformatics online.

Original language	English
Pages (from-to)	4402-4404
Number of pages	3
Journal	Bioinformatics
Volume	35
Issue number	21
DOIs	https://doi.org/10.1093/bioinformatics/btz258
Publication status	Published - 1 Nov 2019
Externally published	Yes

Bibliographical note

© The Author(s) 2019. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Keywords

multiple-genome
Phage Annotation
Toolkit
Evaluator
multiPhATE
de novo phage gene
Yersinia pestis
PhATE
sequence
command-line

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10.1093/bioinformatics/btz258Licence: CC BY-NC

Published versionFinal published version, 114 KBLicence: CC BY-NC

Cite this

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title = "multiPhATE: bioinformatics pipeline for functional annotation of phage isolates",

abstract = "Summary: 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. Availability and implementation: multiPhATE was implemented in Python 3.7, and runs as a command-line code under Linux or Unix. multiPhATE is freely available under an open-source BSD3 license from https://github.com/carolzhou/multiPhATE. Instructions for acquiring the databases and third-party codes used by multiPhATE are included in the distribution README file. Users may report bugs by submitting to the github issues page associated with the multiPhATE distribution. Supplementary information: Supplementary data are available at Bioinformatics online.",

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note = "{\textcopyright} The Author(s) 2019. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com ",

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AU - McNair, Katelyn

AU - Hamilton, Theron

AU - Edwards, Robert

AU - Souza, Brian

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N2 - Summary: 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. Availability and implementation: multiPhATE was implemented in Python 3.7, and runs as a command-line code under Linux or Unix. multiPhATE is freely available under an open-source BSD3 license from https://github.com/carolzhou/multiPhATE. Instructions for acquiring the databases and third-party codes used by multiPhATE are included in the distribution README file. Users may report bugs by submitting to the github issues page associated with the multiPhATE distribution. Supplementary information: Supplementary data are available at Bioinformatics online.

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SP - 4402

EP - 4404

JO - Bioinformatics

JF - Bioinformatics

IS - 21

ER -

multiPhATE: bioinformatics pipeline for functional annotation of phage isolates

Abstract

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Keywords

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