paper.md

title	tags	authors	date	bibliography
GFF3toEMBL: Preparing annotated assemblies for submission to EMBL	bioinformatics annotation EMBL	name orcid affiliation Andrew J. Page 0000-0001-6919-6062 Pathogen Informatics, Wellcome Trust Sanger Institute name orcid affiliation Sascha Steinbiss 0000-0002-2151-0574 Pathogen Informatics, Wellcome Trust Sanger Institute name affiliation Ben Taylor Pathogen Informatics, Wellcome Trust Sanger Institute name orcid affiliation Torsten Seemann 0000-0001-6046-610X University of Melbourne name orcid affiliation Jacqueline A. Keane 0000-0002-2021-1863 Pathogen Informatics, Wellcome Trust Sanger Institute	19 Sept 2016	paper.bib

Summary

An essential part of open reproducible research in genomics is the deposition of annotated de novo assembled genomes in public archives such as EMBL/GenBank [@BLAXTER2016]. The interfaces provided by the major archives do not allow for data to be easily submitted on a large scale without substantial prior knowledge on the part of the submitter. This has lead to a situation where less than 15% of all sequenced bacteria have corresponding public assemblies. We address this by providing GFF3toEMBL, which converts the output of the most commonly used automatic annotation tool, Prokka [@SEEMANN2014], and converts it to a format suitable for submission to EMBL. Built on the GenomeTools annotation processing library [@GREMME2013], GFF3toEMBL is robust, fast, memory efficient and well tested, and has been used to submit more than 30% of all annotated genomes in EMBL/GenBank [@PAGE2016]. It is a small, but essential missing step in making genomic research more open and reproducible.

References