As of March 2024, NCBI’s Genome Workbench, a desktop software suite of tools for visualizing and analyzing molecular sequence data, will no longer be available for download. Due to low usage of this product, we are focusing our effort on newer and more popular resources and tools.
If you have an existing version of Genome Workbench, you can continue to use it, but we will no longer provide customer support, software updates, or tutorial documentation. We will make no additional public releases or updates after March 2024. Continue reading “NCBI’s Genome Workbench to Retire March 2024”
If you use Sequin to submit prokaryotic or eukaryotic genome sequences to GenBank, you need to be aware that Sequin will be retired in January 2021. Genome Workbench’s Submission Wizard, which is already available for submitting annotated genomes, will be the submission tool to use for annotated genomes going forward.
Genome Workbench is desktop software that offers a rich set of integrated tools for studying and analyzing genetic data. You can explore and compare data from multiple sources, including the NCBI databases or the your own private data. The Submission Wizard, available since 2019, allows you to prepare submissions of single genomes where all sequences come from the same organism. This interface (Figure 1) is particularly valuable for:
- Eukaryotic genomes with annotations, for example those prepared with tbl2asn
- Prokaryotic genomes annotated by non-NCBI tools including Prokka and RAST.
Please register to attend our webinar on November 18 to see how to use Genome Workbench to prepare a submission.
(Note: You should continue to submit organelle and viral genomes using BankIt. Please visit the Submission Portal page for information on other submission options.)
Figure 1. Genome Workbench and Submission Wizard. Once the Sequence Editing package is enabled the Submission menu can open the Genome Submission Wizard that prompts you to upload sequence data and presents a tabbed set of forms for entering information about the submission. The Wizard validates the submission and provides editing capabilities for correcting errors. Continue reading “Genome Workbench Submission Wizard to replace Sequin for prokaryotic and eukaryotic genome submissions in January 2021”
Version 3.5.0 of Genome Workbench, NCBI’s sequence annotation and analysis platform, includes two new features. First, we improved the phylogenetic reconstruction algorithm to add sequence additional meta-information, such as isolation source, collection date, and country. This is useful for analyzing coronaviruses, for example. For more information on this feature, check out our new tutorials: creating phylogenetic tree starting from search and creating phylogenetic tree from a multiple alignment.
Second, we made tooltip improvements in the Graphical Sequence View to include information about insertions and unaligned data.
Bug fixes and Improvements
We made a number of other fixes and improvements. In Text View we fixed a crash in showing certain AGP data. With AGP export, we fixed an issue where sequence IDs from AGP did not match sequence IDs from FASTA file (when sequence ranges were used).
In Tree View, we fixed a crash on search and a tooltip issue where tooltip meta-information disappeared when a custom label was set. We also improved startup time and fixed some visual issues in tooltips in the Graphical Sequence View.
Finally, in the Editing Package, we modified the control layout in the Table Reader dialog to fit onto small screens; improved the speed of Table Reader; and fixed several cases for when Undo did not work after importing a feature table.
Version 3.4.1 of Genome Workbench, NCBI’s sequence annotation and analysis platform, includes new features for the Multiple Sequence Alignment View, the Graphical Sequence View and the Sequence Editing and Submission Package as well as a number of other improvements and bug fixes.
In the Multiple Sequence Alignment View, you can now export publication quality graphics (Save As PDF/SVG … , Figure 1). In the Graphical Sequence View you can now search by locus tag, use improved search capabilities for genes by locus and can better display the selected location in the feature editing dialog when annotating a sequence.
Figure 1. A multiple alignment view in Genome Workbench highlighting the new ability to save presentation quality image files (Save As PDF and SVG formats).
In the Sequence Editing and Submission Package, we rearranged the controls in the Table Reader dialog to fit onto smaller screens and improved importing feature tables that contain mat-peptides (mature peptide) features.
Bug Fixes and Improvements
We have made a number of other fixes and improvements. For MacOS users we fixed blurry text in some dialogs, fixed the copy to clipboard problem, and improved support for the latest Catalina version. We also fixed a crashing problem in the Active Object Inspector interface. You should also see improvements in loading SNP data and better recovery in cases of power outages or other events causing local file corruption.
In the Sequence Editing and Submission Package, we fixed a bug that occurred when applying miscellaneous descriptors and structured comment fields using the Table Reader and an issue with using a PubMed ID to look up a publication.
Please see the extensive help documentation including FAQs, videos, and tutorials linked to the Genome Workbench homepage for more information and examples on how to use Genome Workbench in your research.
If you’re interested in visualizing and analyzing genomic data, then you’ll want to check out a new way to run Genome Workbench: in the cloud! Genome Workbench is a desktop application (both Windows and Mac) that lets you analyze genomic data in one place. You can run tools such as BLAST and create views such as multiple sequence alignments, and much more. You can run Genome Workbench on a cloud environment from your local desktop computer. This manual will show you how.
There are many advantages to using Genome Workbench in the cloud:
- You can easily compare your data to the complete GenBank and RefSeq datasets without needing to download them
- You can run BLAST searches against standard databases or any custom databases you’ve assembled in the cloud
- All of the data (e.g. FASTA, BAM, GFF files) remain in the cloud with no need for local copies
- You won’t pay egress fees for downloading data
Give it a try and let us know how it goes!
Here are the latest videos on our YouTube channel. Subscribe to get alerts for new videos.
Genome Workbench version 3 is a major upgrade, including the addition of the Genome Submission Wizard. This video guides you through the wizard, from uploading your genome data file to completion of the submitter report, which is ready to submit to GenBank using tools such as Submission Portal or BankIt. Note: An on-line tutorial is under “Manuals” on the Genome Workbench home page.
Continue reading “NCBI on YouTube: new videos on PubMed, My Bibliography, sequence data and more”
Genome Workbench version 3.0 (release notes) is now available. An important new feature is the submission preparation wizard that allows you to prepare prokaryotic and eukaryotic genome sequences for submission to GenBank. This wizard is the first step toward offering a better alternative to the Sequin submission tool.
You simply load your sequences into Genome Workbench and use the submission wizard to enter information about your submission through a set of dialog boxes and then save a submission-ready data file. The package also includes tools for editing your sequences, annotation, and metadata.
See the tutorial video on our YouTube channel or the Genome Workbench documentation for more details on how to enable the wizard and prepare a submission.
The Genome Workbench team is proud to present version 2.13.0, with the latest usability improvements and bug fixes. See the full list of changes in the Genome Workbench release notes.
Some of the improvements include:
- New SNP tracks using the most recent dbSNP release
- Improved alignment statistics table to correctly account for introns
- Alignment tooltips report introns separately from gaps
- Fixes for several interface issues to make MAFFT and BLAST alignments easier to use.
Genome Workbench is an integrated application for viewing and analyzing sequences. Genome Workbench can be used to browse and import data from NCBI and combine it with your own private data.
The Genome Workbench team is proud to present version 2.12.8, with the latest usability improvements and bug fixes. See the full list of changes in the Genome Workbench release notes.
Some of the improvements include:
- Improved FASTA format view (context menu) and the addition of a “Expand All” option
- Improved rendering of internal unaligned regions
- Automatically open the target folder to export files quickly
- Installation of automatic PROXY detection
- Fixed bug in OS version
Genome Workbench is an integrated application for viewing and analyzing sequences. The Genome Workbench can be used to browse data in GenBank and combine data with your own private data.
Recent updates to Genome Workbench include a new navigation tutorial for Graphical Sequence View, and various bug fixes and improvements. You can see the full list of changes in the Genome Workbench release notes.
Genome Workbench is an integrated application for viewing and analyzing sequences. Genome Workbench can be used to browse data in GenBank and combine this data with your own private data.