Introduction to the template Narrative

Background

KBase and the American Society for Microbiology have created a Narrative template to assist KBase users in publishing genomes as data sets in Microbiology Resource Announcements (MRA). The template follows the MRA Author Checklist for prokaryotic or eukaryotic genome sequences.

For full submission information, please refer to the MRA website. We also recommend reading MRA Best Practices editorial for advice directly from the MRA editors, and which has been used to provide guidance in this Narrative.

For general advice on creating genome announcement Narratives, see this KBase News post by Ben Allen, Miriam Land, and Elisha Wood-Charlson.

Purpose

The goal of this template Narrative is to help you organize your analysis and ensure your documentation matches what is required for MRA submission. It is only meant to provide a guideline for creating a genome announcement publication; you should use it however best works for you - alongside your analysis, copied and pasted into a work document to serve as a template, or in-line with your analysis. You can use the template as it is from the beginning of your analysis, or you can start your analysis in a blank Narrative and add Markdown cells matching these after you have run the apps. You should also feel free to delete any of the text or checkboxes out of the Markdown cells, but keep in mind that these are MRA's requirements for submission, so be sure to include them in your manuscript.

Using the Narrative

This Narrative is a template only. To start, make a copy of this Narrative and follow the organizational structure provided below. You can delete this cell and any extraneous text, including the check boxes, prior to submission.

Apps have not been added to the Narrative. Each section provides recommendations in the "Note to Author" sections, which can also be removed prior to submission. These provide tips for performing the relevant steps in KBase.

Any bold text denotes tips from the MRA Best Practices editorial or the MRA article template. These are required for the resource announcement publication but not the Narrative; however, they can only help to make the Narrative more user-friendly, so we recommend including them here as well once the text has been written. As these are required to submit the article, you can use this Narrative to begin the publication in parallel with your analysis in KBase.

At the end of the analysis sections there are instructions for submission and next steps after completing the analysis in the Narrative.

We've included a list of resources below for working with markdown cells and for creating high-quality MRA publications.

For an example of a previous MRA submission with associated Narrative, see Jennifer Goff et al, Complete Genome Sequence of Bacillus cereus Strain CPT56D-587-MTF, Isolated from a Nitrate- and Metal-Contaminated Subsurface Environment and the Narrative.

This template is currently in a beta state, and as such we would love to hear any feedback or suggestions you have.

Table of contents

1. Tips, Help, and Resources: links to guides and other help resources with Markdown/HTML formatting, MRA Best Practices Guide, etc.
2. Analysis: the sections of the Narrative to keep in the final product
   1. Introduction - Markdown cell for the introductory part of the core MRA Narrative
   2. Background and Experimental Methods
   3. Import
   4. QC, Assembly, and Annotation
   5. Taxonomic Identification
   6. Metabolic Modeling and Flux Balance Analysis
   7. References
3. Final Steps: the next steps for progressing toward an MRA publication, including advice for the non-KBase requirements.

Tips, Help, and Resources

• Markown/HTML Cheat Sheet Narrative: contains helpful examples of markdown and HTML syntax that you can copy and paste into your Narratives
• External guides:
• HTML: HTML offers more options for customization, but it less human readable and simple
• Markdown: Markdown is simpler and more human readable, but has fewer options
• MRA Best Practices Guide: an editorial from the MRA editors with tips and guidance for producing a high-quality MRA publication.
• Examples of published resource announcements in MRA: table in the best practices editorial with examples of different MRA resource types.

Title

Publication Title should not exceed 54 characters. Narratives and articles should have related but different names for enhanced findability.

Abstract

Abstracts for MRA announcements should be limited to 50 words or fewer.

Introduction

Include an introduction to the Narrative including background information on the organism's relatives and where the organism was collected. The publication by [author list] can be found here: [URL]

Table of Contents

1. Background and Experimental Methods
2. Import and annotation
3. QC, Assembly, and Annotation
4. Taxonomic Classification
5. Metabolic Modeling and Flux Balance Analysis
6. References

Narrative created by: [Narrative owner's name and contributors]

Note to Authors

The publication may not be available at the time of the static Narrative creation. This can be added after the fact; please contact engage@kbase.us to update the DOI landing page when this is done.

Background and Experimental Methods

Authors should use this space to detail the experimental methods used to collect, isolate, and sequence the samples.

Author Checklist

A rationale or significance for the sequencing.
The provenance for the sample sequenced and information about the environment.
Detailed methods for DNA isolation, library preparation, and sequencing (including the technology and chemistry used).
Relevant statistics for the sequencing run (e.g., read length and number of reads in total).
Accession numbers for both the assembly and raw reads, each hyperlinked to the publicly available data record.

Sample Collection

Isolation

Genome Sequencing

QC, Assembly, Binning, and Annotation

Author Checklist

A description of how the reads were quality controlled.
Details on how the metagenome was assembled and, if applicable, annotated.
Relevant statistics for the assembly (e.g., number of contigs and N50 values).

Details on how the reads or contigs were binned.
Genome GC content and total size.

Note to authors

The recommended app for quality control is FastQC. There are multiple apps for assembly.

There is no "best" assembler, and assembly tools should be evaluated on a case-by-case basis. You are welcome and encouraged to use multiple apps and compare the results.

Likewise, there are multiple apps that can perform binning, such as MaxBin and MetaBat. Bin quality can be assessed using CheckM and bins can be filtered based on CheckM's assessments using the Filter Bins by Quality with CheckM app.

Within KBase, bins must be extracted as Assembly objects to be annotated.

Annotation can be performed using Prokka or RAST. Again, comparison of multiple tools is encouraged. For downstream steps such as metabolic modeling, however, RAST-annotated genomes perform better with KBase modeling tools.

Import

Note to authors

Reads or assemblies should be imported through the staging area. See the upload and download guide on the KBase documentation site for details instructions.

Taxonomic Identification

Taxonomic identification down to genus for prokaryotic isolates.

Note to Authors

One common way is to use the GTDB-Tk classify app. We recommend adding a phylogenetic tree using the Insert Genome into SpeciesTree app.

Metabolic Modeling and Flux Balance Analysis (optional)

Note to Authors

Metabolic modeling is not listed on the MRA checklist; however, many MRA authors using KBase have included a metaboic model in their Narrative. If you are new to metabolic modeling, we have tutorials and webinars on the docs site and on YouTube.
If you do not use this section, delete this Markdown cell, and remove it from the table of contents at the top of the Narrative.

References

A citation and version number for every piece of software used.

Note to authors

The KBase static Narrative service automatically generates a list of citations for apps used. If you provide any citations for literature or outside tools within the markdown cells, those should be included here.

Final Steps

Requesting a DOI

Once you have completed the analysis steps in KBase and are ready for a public Narrative DOI, send an email to Zach Crockett (crockettzr@ornl.gov) and CC Elisha Wood-Charlson. You should delete the top two cells (Introduction to the Narrative and Resources) and this cell before finalizing the Narrative, and remove any pre-filled text from the other Markdown cells. To get a DOI, we will need a public landing page in the form of static Narrative. To create a static Narrative, make the Narrative public, then select the "Manage Static Narratives" option under the Share menu (see documentation for more information). We will also need some additional metadata not captured in the Narrative, which we will request through the email. If you are not ready to make the Narrative public but do want to start the DOI process, we can reserve a DOI which you can use as when writing the manuscript, but which is not publicly available. Please reach out to us if you have any questions and/or are ready to create or reserve a DOI.

Using a "Dataset" DOI

The external infrastructure that tracks and records relations between citable scientific products only includes the references section, which is sent as structured metadata from the publishers. As such, you must include your Narrative DOI in the references for the bibliometrics infrastructure to recognize it.

This requirement is to enable the machine-readability of the references, but in general the intuitive place to provide a link to the Narrative is in data availability statement. It is perfectly acceptable and even recommended to provide the Narrative DOI in both places as there is no risk of duplicating citation counts between the human- and machine-readable references.

When referring to the Narrative, use the DOI instead of the URL for the static Narrative. We can and will edit the DOI so that it resolves to the most recent version, and this provides forward compatibility in case we ever need to change the URL format for static Narratives.

Depositing in NCBI

Most users deposit reads in the NBCI Sequence Read Archive (SRA). To submit at SRA, login to their Submission Portal. The portal walks users through the steps required for submission, but the metadata submission can be difficult to format correctly. NCBI uses the Minimum Information about any (x) Sequence (MIxS) templates for submission. MIxS is not single template but a collection of templates for different sequence types, such as genomes (MIGS) or metagenomes (MIMS). We recommend reading the MIxS publication to learn more about formatting metadata for the templates. The SRA Submission Portal will help choose which template fits your data.