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DFAST: a Flexible Prokaryotic Genome Annotation Pipeline for Faster Genome Publication

Overview
Journal Bioinformatics
Publisher Oxford University Press
Specialty Biology
Date 2017 Nov 7
PMID 29106469
Citations 615
Authors
Yasuhiro Tanizawa
Takatomo Fujisawa
Yasukazu Nakamura
Affiliations
Soon will be listed here.
Abstract

Summary: We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7000 jobs have been processed since its first launch in 2016. Here, we present a newly implemented background annotation engine for DFAST, which is also available as a standalone command-line program. The new engine can annotate a typical-sized bacterial genome within 10 min, with rich information such as pseudogenes, translation exceptions and orthologous gene assignment between given reference genomes. In addition, the modular framework of DFAST allows users to customize the annotation workflow easily and will also facilitate extensions for new functions and incorporation of new tools in the future.

Availability And Implementation: The software is implemented in Python 3 and runs in both Python 2.7 and 3.4-on Macintosh and Linux systems. It is freely available at https://github.com/nigyta/dfast_core/under the GPLv3 license with external binaries bundled in the software distribution. An on-line version is also available at https://dfast.nig.ac.jp/.

Contact: yn@nig.ac.jp.

Supplementary Information: Supplementary data are available at Bioinformatics online.

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