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 Jacqueline A. Keane 0000-0002-2021-1863 Pathogen Informatics, Wellcome Trust Sanger Institute	19 Sept 2016	paper.bib

Summary

An essential part of open reproducable research in genomics is the deposition of annoated 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 annotation tool, PROKKA [@SEEMANN2014], and converts it to a format suitable for submisison to EMBL. It is robust, fast, memory efficient and well tested, and has been used to submit more than 30% of all annoated genomes in EMBL/GenBank [@PAGE2016]. It is a small, but essential missing step in making genomic research more open and reproducable.

References