Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity David A. Baltrus, a Christina A. Cuomo, b John J. Dennehy, c,d Julie C. Dunning Hotopp, e,f,g Julia A. Maresca, h Irene L. G. Newton, i David A. Rasko, e,f Antonis Rokas, j,k,l Simon Roux, m Jason E. Stajich n a School of Plant Sciences, University of Arizona, Tucson, Arizona, USA b Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA c Queens College of The City University of New York, Queens, New York, USA d The Graduate Center of The City University of New York, New York, New York, USA e Institute for Genome Sciences, University of Maryland Baltimore, Baltimore, Maryland, USA f Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, Maryland, USA g Greenebaum Comprehensive Cancer Center, University of Maryland Baltimore, Baltimore, Maryland, USA h Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware, USA i Department of Biology, Indiana University, Bloomington, Indiana, USA j Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA k Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, USA l Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA m DOE Joint Genome Institute, Walnut Creek, California, USA n Department of Microbiology and Plant Pathology and Institute for Integrative Genome Biology, University of California—Riverside, Riverside, California, USA ABSTRACT Descriptions of resources, like the genome assemblies reported in Microbiology Resource Announcements, are often frozen at their time of publication, yet they will need to be interpreted in the midst of continually evolving technolo- gies. It is therefore important to ensure that researchers accessing published re- sources have access to all of the information required to repeat, interpret, and ex- tend these original analyses. Here, we provide a set of suggestions to help make certain that published resources remain useful and repeatable for the foreseeable future. T here are many ways to sequence and assemble a genome, with the number of available sequencing and assembly platforms seemingly growing every week. Within sequencing platforms, library preparation, chemistry, and error profiles frequently change. Our primary goal as Microbiology Resource Announcements (MRA) editors is to ensure that a manuscript’s techniques and protocols are thoroughly documented so that readers can understand the strengths and weaknesses not only of a particular genome assembly but also the underlying raw data. Given the importance of clarity of workflows and reproducibility of data in validating scientific results (1–3), we want to ensure that all of the relevant data contributing to an assembly are available for other researchers so that they can (i) reproduce the study’s results, (ii) elaborate and incorporate the available data into other genome assemblies, or (iii) repurpose public data for use in alternative analyses. While many of these current best practices have been incorporated into the Instructions to Authors, in this opinion piece, we aim to provide a set of thematic ideas and examples behind certain instructions for authors to increase reproducibility across groups and utility for future users. We also highlight the fact that groups have proposed sets of standards for isolate genomes (4), 16S rRNA/18S rRNA/other amplicons (5), and single-cell amplified genomes (SAGs) and metagenome- assembled genomes (MAGs) (6) and that recommendations from those proposals are highly relevant and compatible with points raised in this editorial. Citation Baltrus DA, Cuomo CA, Dennehy JJ, Dunning Hotopp JC, Maresca JA, Newton ILG, Rasko DA, Rokas A, Roux S, Stajich JE. 2019. Future-proofing your Microbiology Resource Announcements genome assembly for reproducibility and clarity. Microbiol Resour Announc 8:e00954-19. https://doi.org/10.1128/ MRA.00954-19. Copyright © 2019 Baltrus et al. This is an open- access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to David A. Baltrus, baltrus@email.arizona.edu. The views expressed in this Editorial do not necessarily reflect the views of the journal or of ASM. Published 5 September 2019 EDITORIAL crossm Volume 8 Issue 36 e00954-19 mra.asm.org 1