Dataset Information

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.

SUBMITTER: Ecale Zhou CL

PROVIDER: S-EPMC6821344 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Publications

multiPhATE: bioinformatics pipeline for functional annotation of phage isolates.

Ecale Zhou Carol L CL Malfatti Stephanie S Kimbrel Jeffrey J Philipson Casandra C McNair Katelyn K Hamilton Theron T Edwards Robert R Souza Brian B

Bioinformatics (Oxford, England) 20191101 21

<h4>Summary</h4>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. ...[more]

PMID: 31086982

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