Introducing the NIH Comparative Genomics Resource (CGR)

NCBI is looking forward to seeing you in person at the International Plant and Animal Genome Conference (PAG XXIX), January 8-12, 2022 in San Diego, California. We’re especially excited to introduce our newest endeavor – the NLM initiative known as the NIH Comparative Genomics Resource (CGR)– a platform we are developing to support comparative analyses of sequenced eukaryotic research organisms. Understanding and supporting the needs of researchers is a fundamental element in the development of CGR and is critical to its future success in supporting a large and diverse collection.

Please join NCBI for the following events to learn more about CGR and how you can inform its development:

Important Note: The listed times are Pacific time.

Workshop: NCBI Resources for Genomic Research
Monday, January 10 at 12:50 – 3:00 PM

The CGR initiative is underway at NCBI to elevate comparative genomics resources, promote high-quality data submission and re-use, offer the best and most complete content, and support efficient and effective scientific discovery. This workshop will provide an overview of advances at NCBI, including genome submission, contamination screening, genome annotation, and data access through NCBI Datasets and the new organism portal, and Genome Data Viewer.

12:50 – 1:10 PM – The Comparative Genomics Resource Initiative at NCBI
Presenting Author: Valerie A. Schneider, Ph.D

1:10 – 1:30 PM – Genbank Submission: How Do I Submit My Data to NCBI?
Presenting Author: Shelby Bidwell

1:30 – 1:50 PM – Rapid Detection of Genome Assembly Contaminants using New Tools from NCBI
Presenting Author: Eric Tvedte, Ph.D

1:50 – 2:10 PM – Advances in Genome Annotation from NCBI RefSeq
Presenting Author: Vamsi Kodali, Ph.D

2:10 – 2:30 PM – NCBI Datasets, a New Resource for Retrieving Comparative Genomic Data
Presenting Author: Nuala A. O’Leary, Ph.D

2:30 – 2:50 PM – Expanding the Scope of NCBI’s Genome Data Viewer
Presenting Author: Sanjida Rangwala, Ph.D

Listening Session:
A Conversation with NCBI about the NIH Comparative Genomics Resource (CGR)
Tuesday, January 11 at 9:30 – 10:30 AM

This is an opportunity for you to provide your feedback on how the CGR platform can best support your research needs. We also want to learn about existing tools that are essential to your work that should be included in the platform as well as new tools we can prioritize for development. Note: this listening session is in conjunction with PAGXXIX.

Booth #421, Exhibit Hall

Stop by our booth to provide feedback, ask questions, or just to chat!

Sunday, January 9, 3:00 PM – 8:30 PM
Monday, January 10, 9:30 AM – 5:00 PM
Tuesday, January 11, 9:30 AM – 3:00 PM

Additional NCBI Talks:

Saturday, January 8

1:05 – 1:25 PM – Datasets, a New Resource That Lets You Easily Gather Data from Across NCBI Databases

This presentation will focus on NCBI Datasets, an interface for accessing genome, gene, and ortholog data through a redesigned website and command-line tools. We will guide you through the process of incorporating NCBI Datasets into bioinformatic analysis workflows.

2:10 – 2:30 PM – New Resources Supporting Genome Analyses from NCBI

NCBI is developing a new resource to help researchers with comparative genomics analyses. The data structures, tools, and interfaces of CGR will enable wider reuse of the more than twenty-thousand eukaryotic genome assemblies from nearly nine thousand species, and related genomics content available from NCBI and enhance their connectivity to other resources.

3:00 – 3:30 PM – Updates to the Chicken Genome Resource and Annotation

Discover more about chicken genome and annotation resources at NCBI during this presentation. NCBI provides high-quality gene predictions produced by the Eukaryotic Genome Annotation Pipeline (EGAP), supplemented with manual expert curation for a subset of model organism genomes such as chicken. The products of EGAP annotations for chicken, along with more than 800 other eukaryotes are available across multiple NCBI resources, including Gene, BLAST, and Genome Data Viewer (GDV).

Sunday, January 9

11:00 – 11:20 AM – Update on NCBI Annotation Efforts on Sheep and More

Annotated high-quality reference genomes are critical for developing hypotheses for the genetic underpinnings of observed natural variation. During this presentation, we will show how this data substantially improved the accuracy of TSSs in nearly 50,000 transcripts (46,000 of them coding) for nearly 17,700 genes. In addition, we will lay out the vision for the NIH Comparative Genome Resource (CGR), an organism-agnostic platform that will facilitate submission, annotation, visualization, and access to data.

12:10 – 12:30 – Visualization and Analysis of Solanaceae Genomes at NCBI

As part of our initiative to better support comparative genome analysis, NCBI has made several updates to the Genome Data Viewer. We are happy to work with members of the community to make sure that your favorite assemblies are available to view at NCBI. As part of this presentation, we’ll discuss our plans for this tool to gather audience feedback to ensure that we meet the needs of Solanaceae researchers.

5:22 – 5:42 PM – NCBI Tools for Whole-Genome Annotation

Join this presentation to learn how you can quickly add high-quality gene annotation to your bacterial and archaeal assemblies. NCBI’s goal is to offer annotation tools that are easy to use and produce a quality product on draft or finished genomes. During this presentation, we will highlight a few key NCBI tools for whole-genome annotation, such as the Prokaryotic Genome Annotation Pipeline (PGAP) and the Read assembly and Annotation Pipeline Tool (RAPT). We will also introduce NCBI’s plans for a stand-alone eukaryotic annotation pipeline that will be developed in the context of the NIH CGR.


Monday, January 10 at 10:00 – 11:30 AM

Advances in Genome Annotation from NCBI Refseq – PE0026
Introducing NCBI’s New Portal for Genome Data Access – PE0070
Rapid Detection of Genome Assembly Contaminants Using New Tools from NCBI – PE0072
The Comparative Genomics Resource Initiative at NCBI – PE0122

Monday, January 10 at 3:00 – 4:30 PM

NCBI Datasets, a New Resource for Retrieving Comparative Genomic Data – PO0069
NCBI Blast: Recent Update to Facilitate Organism-Focused Searches – PO0071
Genbank Submission: How Do I Submit My Data to NCBI? – PO0073
Expanding the Scope of NCBI’s Genome Data Viewer – PO0121

To stay up to date on all NCBI activities at PAGXXIX, follow us on Twitter at @NCBI.

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