CLC Genomics Workbench: baixar versions anteriors

Improvements
- Automatic opening of a browser when following a web link from the Workbench, including when using QDI online licensing, is supported for more Linux desktops.
- Various minor improvements
Bug fixes
- Fixed an issue causing EMBL formatted nucleotide sequences containing two or more different symbols apart from AGCTN to be imported as peptide sequences in earlier versions in the 26 release line.
- Fixed an issue affecting the ability to mark sequences in alignments or sequence lists in earlier versions in the 26 release line. In affected versions, marking was treated as synonymous with the selection of all the residues in a sequence. This affected the actions that could be taken on marked sequences, and had the effect that, after checking selection boxes to mark sequences, a click elsewhere in the graphical view or in a linked table view, would clear the marked status of all other sequences, and would mark the sequence clicked on. In addressing this issue, a number of changes have been introduced. These are listed in the Changes section of the release notes.
- The flashing effect observed when the mouse cursor was moved across selected regions of sequences has been removed. This affected earlier versions in the 26 release line, and could be observed in elements such as alignments and sequence lists.
- Fixed an issue affecting alignments in earlier releases in the 26 release line, where a region of an individual sequence could be deleted from the view opened using the right-click option in the Table view, "Open This Sequence".
- Various minor bugfixes
- Vulnerabilities fixed in this release include:
- CVE-2026-49844
- CVE-2026-59903
Changes
- The bundled Java version is Java 21.0.12.1, where we use the JRE from the Azul OpenJDK builds.
- When working in the graphical view of an alignment or sequence list:
- Marking sequences can be done by clicking once on a sequence name, and unmarked by clicking again on the sequence name. This correspondingly selects the selection boxes that can be displayed by checking the "Show selection boxes" option in the Side Panel.
- The names of marked sequences are highlighted.
- The "Delete Marked Sequences" option, removed in earlier versions in the 26 release line, has been re-introduced in the context menu opened with a right-click on a sequence label or sequence content.
- When working with linked graphical and table views of a sequence list or alignment, selecting a row in the table view selects all the residues in the corresponding sequence in the graphical view. It does not affect the marked status.
Advanced notice
- The AGP export (legacy) tool will be retired in a future version of the software.
- The legacy Workbench policy property 'run_on_workbench_when_server_is_available' will not be supported from version 27.0. The workbench_save_to_server policy property, available since version 25.0, should be used instead.
- Installers for Intel macs will no longer be provided from June, 2027.

QIAGEN CLC Genomics Workbench 26.0.5
Bug fixes
- Fixed an issue where double-clicking an annotation in the circular view of a sequence selected all symbols instead of just those overlapping the annotation.
- Fixed an issue causing workflows to look pixelated in the Workflow Editor canvas and the Minimap in the Side Panel when using a scaled monitor (e.g. an HiDPI monitor).
- Fixed an issue where QDI Licensing could not be used if the Workbench was configured to use a proxy that requires authentication.
- Various minor bug fixes
- Vulnerabilities fixed in this release include:
- CVE-2026-9828
- CVE-2026-54512
- CVE-2026-54513
- CVE-2026-54514
- CVE-2026-54515
- CVE-2026-47244
- CVE-2026-44249
- CVE-2026-45416
- CVE-2026-48043
- CVE-2026-50020
- CVE-2026-50560
- CVE-2026-50010
- CVE-2026-56745
- CVE-2026-56746
- CVE-2026-56819
- CVE-2026-55831
- CVE-2026-55833
- CVE-2026-59898
- CVE-2026-59899
- CVE-2026-59900
- CVE-2026-59901
- CVE-2026-59921
- CVE-2026-59949
Changes
The bundled Java version is Java 21.0.12, where we use the JRE from the Azul OpenJDK builds.
Advanced notice
- The AGP export (legacy) tool will be retired in a future version of the software.
- The legacy Workbench policy property 'run_on_workbench_when_server_is_available' will not be supported from version 27.0. The workbench_save_to_server policy property, available since version 25.0, should be used instead.

Bug fixes
- Fixed an issue where mouse-based range selection did not work in the cloning editor.
- Fixed an issue where the SAM/BAM/CRAM Mapping Files importer failed for long reads starting with an unaligned region longer than twice the circular reference length.
Changes
The bundled Java version is Java 21.0.10, where we use the JRE from the Azul OpenJDK builds.
Advanced notice
- The AGP export (legacy) tool will be retired in a future version of the software.
- The legacy Workbench policy property 'run_on_workbench_when_server_is_available' will not be supported from version 27.0. The workbench_save_to_server policy property, available since version 25.0, should be used instead.

QIAGEN CLC Genomics Workbench
Improvements
- A link to the Modify a Workflow tutorial, which steps through creation of a customized analysis pipeline by editing an existing workflow, has been added to the Workbench background canvas.
- The minimum coverage of target region positions from QC for Targeted Sequencing reports can be selected for inclusion in reports generated by Create Sample Report and Combine Reports.
- Detect Fusion Genes from DNA adds "Fusion pair" information for fusions reported when "Include all fusions in the track output" is checked but where there is no fusion crossing reads supporting the fusion. This addition provides better support for downstream filtering.
- Iterate workflow elements can now be connected downstream of Differential Expression for RNA-Seq, enabling downstream filtering when multiple statistical comparisons are produced.
- Using left or right arrow navigation buttons in a variant track jumps the focus to the next visible variant. Previously, focus was moved to the next variant, even if it was hidden due to view settings in the Side Panel.
- Exporting PDFs of reports that contain plots with many points is faster than previously.
- Various minor improvements
Bug fixes
- Fixed an issue where Detect and Refine Fusion Genes sometimes output fusions with duplicated "Fusion pair" values when "Include all fusions in the WT track output" was checked. This could cause VCF export to fail and filtering tools to keep or remove too many fusions. See the public notification about this issue.
- Fixed an issue in Create Sequence Constructs where, when a saved Sequence List was used as input and at least three sequences in that list were deselected, roughly half of the deselected sequences would be included in the construct set generated.
- Fixed an issue causing the "Pairwise % identity" value in the Positional stats palette in the Side Panel of alignments to be incorrectly calculated.
- Fixed an issue where the "Read Mapping" output channel from Merge Read Mappings could not be connected to all workflow elements that accept a read mapping as input, e.g. QC for Read Mapping.
- Fixed an issue where the processing order defined for a tool in a workflow was not respected if one or more inputs to that tool originated from a Fork element that had at least one unconnected output channel. This is not expected to affect the substance of results, but could affect ordering within an output, for example, the order of sections in a sample report or the order of tracks in a Track List.
- Fixes relating workflow history information:
- Fixed an issue affecting the history information in outputs generated using installed or template workflows that contained at least one Fork element with all its output channels connected to downstream steps, where the workflow version was reported as 0.0 and no build-id was included. Note that for template workflows, the version of the software delivering that workflow can act as a proxy for the build-id.
- Fixed an issue affecting the history of workflow log elements generated by running a workflow on a CLC Workbench, where the details of the workflow run (name, version, and where relevant, build id) were not present. This problem did not affect log elements generated by analyses run on a CLC Server or on the cloud.
- The following fixes affecting history information in outputs generated by workflows run on the cloud:
- Details of the workflow run (name, version, and where relevant, build id) were not present in the history of Workflow Result Metadata elements.
- History information in outputs generated using installed workflows did not contain the correct workflow build-id.
- History information in outputs from workflows launched from the workflow editor contained a workflow build-id when there should not have been one.
- Various minor bug fixes
- CVEs fixed in this release include:
- CVE-2025-67735
- CVE-2025-12183
- CVE-2025-66566
Plugin notes
Upgrading to CLC Genomics Workbench 26

Bug fixes
- Fixed an issue causing labels for annotations on sequences displayed in "No wrap" mode to not be visible unless the start of the annotation was in view when using a HiDPI or other scaled monitor.
- CVEs fixed in this release include:
- - CVE-2025-31257
- CVE-2025-53066
- CVE-2025-53057
- CVE-2025-61748
Changes
The bundled Java version is Java 21.0.9, where we use the JRE from the Azul OpenJDK builds.
Advanced notice
The AGP export (legacy) tool will be retired in a future version of the software.
Please see the release notes for CLC Genomics Workbench 26.0, below, for a full list of changes since the last general release of this software.

Improvements
- The ClusteredNR peptide database is available to search using BLAST at NCBI.
- Various minor improvements
Bug fixes
- Fixed an issue in Detect and Refine Fusion Genes where reads were incorrectly discarded during the refinement step in cases where an exon flanking the breakpoint was the same length or shorter than the "Breakpoint distance" specified for the analysis. The default distance is 10. This fix leads to an increase in fusion crossing reads and 5'/3' read coverage for affected exons. The issue was most likely to impact fusions with novel exon boundaries.
- Fixed an issue where Structural Variant Caller for Long Reads could report the sequence of an insertion inaccurately, where the start of the insertion was most impacted. Affected sequences were supported by only a small fraction of reads, and were most likely to be observed in noisy, high-coverage datasets.
- Fixed an issue causing QC for Sequencing Reads to fail when the input contained a very small number of long sequences, relative to the total number of sequences in the analysis, and the only output from the analysis was the supplementary report.
- CVEs fixed in this release include:
- CVE-2025-30749
- CVE-2025-50106
- CVE-2025-24855
- CVE-2025-27113
- CVE-2025-30754
- CVE-2025-50059
- CVE-2025-30761
- CVE-2025-48924
- CVE-2025-49128
- CVE-2025-52999
- CVE-2025-25193
- CVE-2025-24970
Reference data related
- Macaca fascularis T2T-MFA8v1.1 was made available for download using Download Genomes in CLC Genomics Workbench 25.x on July 9, 2025.
- Effective July 16, 2025, Download Pfam Database downloaded Pfam 37.4. That update affected downloads using this version and earlier versions of the software.
Changes
The bundled Java version is Java 21.0.8, where we use the JRE from the Azul OpenJDK builds.
Advanced notice
- Correct Long Reads (legacy) will be retired in a future version of the software.
- The policy property ‘run_on_workbench_when_server_is_available’ will be retired in a future release. Please use the workbench_save_to_server policy instead.

Improvements
- Positions in reads that do not match the reference in read mappings are displayed using the defined mismatch colors at all zoom levels, rather than just when zoomed in.
- Data downloaded from an AWS S3 bucket via a CLC Server AWS Connection using the "Download and Save..." option in the Remote Files tab can be downloaded to a CLC Server location or to disk (a CLC Server import/export directory). Previously such downloads could only be saved to a CLC Server location.
- Using the right-click "Upload to This Folder" menu option in the Remote Files tab, data for upload to AWS S3 buckets can be selected from CLC data locations and the local file system. When logged into a CLC Server with one or more valid AWS Connections, data for upload can also be selected from CLC Server locations, and, when an AWS Connection configured on the CLC Server is selected, data can also be uploaded from CLC Server import/export directories. Previously data could only be selected from CLC data locations.
- Improvements made to better support licensing handling for CLC Workbenches run on hardened Linux environment where execution in TEMP is not allowed.
- Various minor improvements
Bug fixes
- Fixed an issue where QC for Targeted Sequencing counted coverage for only one gene when multiple genes overlapped. Coverage is now correctly counted for all overlapping genes.
- Fixed an issue where BLAST at NCBI could fail if the 'Mask low complexity regions' option was unchecked.
- The background color of the 3D Molecule Viewer can again be specified in the Side Panel settings when working with a Molecule Project. This setting was absent in CLC Genomics Workbench 25.0 and 25.0.1.
- Fixed a bug where table rows removed from a selection could be silently added back into the selected set if the table was subsequently sorted based on column values.
- Fixed an issue affecting mRNA tracks generated using Filter on Custom Criteria in CLC Genomics Workbench 24.x or earlier followed by filtering using one or more tools in CLC Genomics Workbench 25.0 or 25.0.1. Such tracks were not recognized as mRNA annotation tracks by tools such as RNA-Seq Analysis.
- Fixed an issue in Annotate with Repeat and Homopolymer Information where repeat element sequences for deletions were occasionally shifted by a base. For example, a deletion of 'TGAA' could be incorrectly reported as a repeat element sequence of 'GAAT'.
- Fixed an issue where Demultiplex Reads could not be run via the CLC Genomics Server when launched from the Tools menu.
- Fixed an issue affecting the second or subsequent use of Associate Data Automatically when associating data with rows of a CLC Metadata Table using the Prefix or Suffix matching scheme. If no changes were made when launching Associate Data Automatically the second or subsequent time in a given Workbench session, the "Exact" scheme was used instead of the selected scheme. The first use of this functionality was unaffected by this problem.
- Various minor bugfixes
- CVEs fixed in this release include:
- CVE-2025-21502
- CVE-2024-21208
- CVE-2024-21210
- CVE-2024-21217
- CVE-2025-21587
- CVE-2025-30698
- CVE-2025-30691
- CVE-2024-47606
- CVE-2024-54534
- CVE-2025-3167
- CVE-2024-12798
- CVE-2024-12801
- CVE-2025-46701
Plugin notes
Fixed an issue in Compare Immune Repertoires, delivered by Biomedical Genomics Analysis, where clonotypes missing a C segment and containing ambiguous segments were not resolved when both resolve options were checked.
Changes
The bundled Java version is Java 21.0.7, where we use the JRE from the Azul OpenJDK builds.
Reference data related
Effective June 18, 2025, Download Pfam Database downloads Pfam 37.3. This update affects downloads using this version and earlier versions of the CLC Genomics Workbench.
Advanced notice
Correct Long Reads (legacy) will be retired in a future version of the software.