Release Notes for Genome Workbench 3.8.0 (August 9, 2022)

New Features:

• CSI index files are now supported for BAM and VCF file uploads
• Added ability to generate a project with different folders for each input ASN.1 object
• New alternative start option for using 'ATG/GTG/TTG' start codons in the six-frame translations track in the Graphical Sequence View
• Added ability to edit steps in the microflow macro editor

Bug fixes and Improvements:

• Fixed a bug preventing pasting a search term in the search box of the Tree View
• Fixed a bug in locating SNP features using the search function in the Graphical Sequence View
• Updated code to be compatible with a new PubMed API
• Additional feature and performance improvements
• Additional minor bug fixes

Release Notes for Genome Workbench 3.7.1 (October 13, 2021)

Bug fixes and Improvements:

• supports 64-bit NCBI GI accessions

Release Notes for Genome Workbench 3.7.0 (August 31, 2021)

New Features:

• GBench can now import GenBank flat files
• GBench is now fully 64-bit GI compatible
• Users can select and copy text from the tooltips in Graphical Sequence View
• Starting position of VCF variants is shown in the Graphical Sequence View tooltips
• Imported dbVar VCF files are colored and have similar information as other dbVar tracks
• FASTA section of GFF3 files is recognized during import
• Users in multiple screen environment have a choice of whether GBench will open its dialogs on the same screen as the main GBench window or on the last used screen
• GBench upgrade checks for a currently running instance of GBench and asks user to close it, proceeding with upgrade when this is done

Bug fixes and Improvements:

• VCF import: now works faster for some kinds of VCF files
• VCF import: better detection of errors when reading streamed VCF files
• VCF import: some technically necessary INFO fields are always imported from VCF files
• Fixed crash on zooming in the Paralogous/pseudo gene alignments tracks
• Corrected selection for broadcasting between span and multi-pane views for gaps
• Fixed a random crash after a long period of inactivity
• Updates and bug fixes in the Genbank submission editing package
• Additional improvements to performance and stability

Release Notes for Genome Workbench 3.6.0 (March 04, 2021)

New Features:

• improved ability to recognize and process large or complex VCF files (tutorial), including ability to view data in the Graphical Sequence Viewer, Active Objects Inspector, and the Generic Table View
• Search View can search for variation IDs from VCF files
• now supports importing of feature tables with a mix of CDS with or without local protein IDs
• updates to documentation pages (e.g. Basic Operation Working with BAM Files and others)
• incorporates SC-25 NCBI shared services package

Bug fixes and Improvements:

• "link mate pairs" display option now works for BAM file data
• index files with .bai extension are now recognized
• fixed a bug in mapping locations for tables with chromosome identifiers
• minor updates and bug fixes in the Genbank submission editing package, including ability to set the location to chromosome in macro, support for BankIt identifiers, and more
• additional improvements to performance and stability

Release Notes for Genome Workbench 3.5.0 (September 3, 2020)

New Features:

• Phylogenetic reconstruction algorithm improved to add sequence additional meta-information like isolation source, collection date, country. Useful for SARS, coronavirus analysis. (see new Creating phylogenetic tree starting from search and Creating phylogenetic tree from precalculated multiple alignment tutorials)
• Graphical Sequence View: tooltip improvements to include information about insertions and unaligned data

Bug fixes and Improvements:

• Text View: fixed crash in showing certain AGP data
• AGP export: fixed issue that sequence ids from AGP does not match sequence ids from FASTA file, when sequence ranges are used
• Tree View: fixed crash on search
• Tree View: fixed tooltip issue that tooltip meta-information disappeared when custom label is set
• Graphical Sequence View: improved startup time
• Graphical Sequence View: fixed some visual issues in tooltips
• Editing Package: modified control layout in the Table Reader dialog to fit onto small screens
• Editing Package: improved speed of Table Reader
• Editing Package: fixed several cases for when Undo did not after importing a feature table

Release Notes for Genome Workbench 3.4.1 (June 8, 2020)

New Features:

• Multiple Sequence Alignment View: implemented export of SVG/PDF vector graphics (poster quality)
• Graphical Sequence View: added Search by locus tag
• Editing and Submission Package: rearranged controls in the Table Reader dialog to fit onto smaller screens
• Editing and Submission Package: improved importing feature tables that contain mat-peptides
• Graphical Sequence View: improved searching for genes by locus-tag

Bug fixes and Improvements:

• Active Object Inspector: fixed crash in the UI.
• MacOS improved support of the latest Catalina version of MacOS
• Improved management of local caches reset it in case of power outage or other events causing local file corruption
• Improved protocol for loading SNP data
• MacOS: improved blurry text in some dialogs
• MacOS: fixed copy to clipboard regression
• Editing and Submission Package: fixed bugs when applying miscellaneous descriptors and structured comment fields using the Table Reader
• Editing and Submission Package: fixed an issue when publication is looked up based on its PMID
• Graphical Sequence View: fixed displaying the selected location in the feature editing dialog when annotating a sequence

Release Notes for Genome Workbench 3.3.1 (March 25, 2020)

New Features:

• Graphical Sequence View: Sequence tracks – improved coloring of gaps of various types of uncertainty, when looking at the Genomes level show gaps annotated in contigs and scaffolds
• Graphical Sequence View: improved display of Genes track to show more genes at high zoom level (previously filtered off)
• Editing and Submission Package: Submission Wizard: make Assembly Method, Genome Coverage and Sequencing Technology fields optional

Bug fixes and Improvements:

• Graphical Sequence View: fixed issues with BAM visualizations, specific to some bacterial samples with only one chromosome and a plasmid
• Graphical Sequence View: show all alignment reads regardless of the MAPQ score including reads with MAPS=0
• Graphical Sequence View: improved import of BAM files, BAM file import dialog reworked to avoid double compute of pile-up, BAM now opens faster

Release Notes for Genome Workbench 3.2.0 (February 10, 2020)

New Features

• Graphical Sequence View: Added search by feature, SNP rsid, position or range
• Added support for PSL alignments format (import)
• Editing and Submission Package: Graphical Sequence View: added ability to edit/delete features.
• Editing and Submission Package: Graphical Sequence View: added gap display (known/unknown/contamination).
• Editing and Submission Package: Graphical Sequence View: added connection from the Validator and the Discrepancy Report.

Bug Fixes and Improvements

• Multiple Sequence Alignment View: fixed visualization bugs
• Editing and Submission Package: Import Feature Table dialog: added export button to report errors.
• Editing and Submission Package: Table Reader dialog: added report of all duplicate rows.
• Editing and Submission Package: Submission menu: added Save ASN.1 file menu item.
• Editing and Submission Package: Add CDS dialog: fix/improvement for annotate CDS to correctly place gene.
• Editing and Submission Package: CDS Editor dialog: fix/improvement for stop-codon retranslation.
• Editing and Submission Package: Sequence Editor: fix/improvement for feature adjustment by mouse drag.
• Editing and Submission Package: Validator dialog: added new handlers for errors SEQ_INST_AllNs and SEQ_INST_InternalNsInSeqRaw.
• Editing and Submission Package: Add Assembly Gaps dialog: fix/improvement in handling code-breaks and anticodons.
• Text View: fixed crash in processing blinking cursor
• MacOS: improved support of Apple SDK 10.14 (Mojave) and Apple 10.15 (Catalina)(MacOS 10.13 High Sierra and earlier versions are no longer supported)
• MacOS: improved support for dark mode
• Improved messaging and diagnostics of situations when data and annotations are loaded into different projects which results in “lcl|” cannot be found messages. Improved documentation on that.

Release Notes for Genome Workbench 3.1.0 (September 30, 2019)

New Features

• Genome Editing and Submission: new update sequence tool to replace/extend/patch an existing sequence with a new one, meanwhile adjusting existing features and importing new ones
• Graphical Sequence View: BAM alignment track – implemented haplotype filtering
• Graphical Sequence View: export of graphics in SVG format

Bug Fixes and Improvements

• MacOS: fixed bacl background visual issues related to Metal API

Release Notes for Genome Workbench 3.0.1 (August 20, 2019)

New Features

• Genome Workbench can now run on Google Cloud or Amazon Web Services platforms (see Running Genome Workbench over X Window System for more details)
• Genome Workbench can now be installed on HPC cluster running on Linux (see Running Genome Workbench over X Window System for more details)
• Genome Workbench can now be used with X Window System (see Running Genome Workbench over X Window System for more details)
• New "Help" buttons implemented in submission editing dialogs

Bug Fixes and Improvements

• Database: VDB gate indexing fixed
• MSA view: expanded features issues fixed
• Assembly: assembly table going blank fixed for MacOS
• Graphical Sequence View: Assembly Accession selection fixed
• Editing Tools: fixed crash in Remove All Features
• Add Publication: fixes for DOI lookup
• Sequences: fixes for Add Assembly Gaps to Sequence
• Editing Tools: fixed crash in Convert Features
• Editing Tools: fix for Retranslate Coding Regions improperly adjusting mat-peptide spans

Release Notes for Genome Workbench 3.0.0 (July 3, 2019)

New Features

• In this version NCBI releases a new extension package to create and edit genomic submissions for GenBank. This new package is supposed to replace NCBI Sequin (see Feature comparison between Sequin and Genome Workbench for more details)
• Documentation for Genome Workbench Editing
• Sequence Editing Package: improved support for GFF3 import files for feature annotation
• New menu items to add, edit, and remove individual features on sequences, functionality to manipulate sequence data. New validator with ability to check against GenBank submission standards and fix problems found.
• Added support for clients working via Windows Remote Desktop
• Extended support for X-Windows protocol, Genome Workbench can now display graphics in X-Windows configuration, tested with X2Go client and other servers
• MacOS: Added build for MacOS Metal graphics to reflect Apple plan to discontinue support for OpenGL in new versions of MacOS

Bug Fixes and Improvements

• Tree View: fixed crash with tree re-routing
• BAM files: fixed SRR accession validation issues in the Open Dialog
• MSA View: fixed minor flickering issues on Windows

Release Notes for Genome Workbench 2.13.0 (March 20, 2019)

New Features

• Graphical Sequence View: new SNP tracks released
• Graphical Sequence View: improved alignment statistics table (Alignment statistics settings: Show A, G, T, C and Gaps) to correctly account for introns (graphics now include intron row)
• Graphical Sequence View: Alignment tooltips now also report introns separately from gaps

Bug Fixes and Improvements

• Graphical Sequence View: fixed bug with incorrect vector graphics (PDF) export in case when default settings were changed
• Graphical Sequence View: improved BAM / SRA renderings of D/N CIGAR specified gaps
• Graphical Sequence View: fixed bug in context menu action “Zoom to Selected Object(s)”
• Text View: fixed crash in Flat File (GenBank) mode, crash was happening because of incorrect handling of diacritic symbols
• Tools MAFFT: fixed issues with running it on MacOS and Windows
• Tools BLAST: Improved MacOS interface to pick blast database file location
• Improved import of FASTA sequences via clipboard

Please see earlier release notes if needed.