New features

• Heat maps: It is now possible to show a legend on a heat map.

Changes

• When importing Genbank nucleotide sequences, the Workbench will determine whether it is DNA or RNA based on the sequence rather than the description in the file.

Bug fixes

• Fixed: Trimming sequencing data for vector contamination from UniVec failed
• Fixed: GFF export failed.
• Fixed: Copying information from the Folder Contents view did not work.
• Fixed: out of memory error when performing bootstrapping with ML tree construction methods.

Bug fixes

• Fixed problem in workflows: it was not possible to configure all elements when running a workflow that branched after the input element.

Bug fixes

• Description text in progress area is now making full use of available width of the progress area
• Handling of line breaks in annotation notes improved
• On Linux: User interface text has been changed to not use bold font to make a better visual appearance
• Annotation tracks and variant tracks created in CLC Genomics Workbench can be displayed in a table

Improvements

• Fragments generated from restriction site analysis can now be opened in batch. When multiple rows in the fragment table are selected, the right-click menu option will now create a sequence list with all the selected fragments.
• For alignments, mappings, BLAST results and other sequence views, the right-click options to Open Copy of Sequence and Open This Sequence have been merged to Open Sequence. If a copy should be created, use Save As with the new sequence, or drag it into a folder in the Navigation Area.

Bug fixed

• Several errors related to workflow configuration and execution have been fixed.
• Errors related to managing Workspaces have been fixed.
• Annotations were added by the Find Open Reading Frames tool, even though the option to add annotations was not selected. This is now fixed.
• Fixed an out-of-memory problem in the Create Alignment tool.

Improvements

• Added Legal and Tabloid formats for printing

Bug fixes

• Fixed an error when translating DNA to protein. When more than 10 sequences were produced, the resulting protein sequence included X instead of * as stop symbol. We advice customers to re-run any analyses with the translation tool when using more than 10 sequences as input.
• Various minor bug-fixes

New features

• Workflow: there are several important new features for workflows
  • It is possible to control which parameters should be locked or unlocked. This means that the creator of the workflow can decide which parameters should be left open for adjustment when the workflow is executed.
  • Usability of workflow editor greatly improved
    • There is a grid for helping layout
    • Visual indication of the number of possible connections as input to a workflow element
    • Visual indication to show if parameters have been changed
    • Handles for dragging and connecting elements have been made more clear
    • Side Panel for controlling grid layout and switching on compact visualization of workflow elements
    • You can high-light selected paths in a workflow
  • It is now an option to attach the workflow design file with the installer to allow users edit the workflow
  • There is a special icon for workflows in the Toolbar to make the creation and installation of workflows more visible
  • Several tools are now workflow-enabled:
    • Find Open Reading Frames
    • Translate to Protein
    • Convert to RNA
    • Convert to DNA
• Toolbox improvements:
  • New Favorite Toolbox: A new tab next to the Toolbox holds
    • Frequently used tools. This is automatically updated based on which tools are used most frequently.
    • Favorite tools: Right-clicking a tool in the Toolbox allows you to add a tool to your favorites list.
  • Quick launch of tools: Pressing Ctrl + Shift + T shows a dialog for easy typing and launching tools.
• Relevant view settings are now copied when switching between different views of the same data. As an example: if you have specified a set of restriction enzymes to display in the circular view of a sequence and switch to the linear view, these enzymes will also be listed in the Side Panel here. Note that the Side Panel settings are only copied to the new view if they have been changed by the user in the old view.
• Performance when sorting of large tables has been improved
• Rename can now be done through right-click menu in Navigation Area.
• Annotations on circular sequences:
  • When shown in linear view they have a cleaner appearance. Before, there was a line from beginning to end of the annotation, and this has now been removed.
  • When shown in circular view, it is no longer displayed as a joined annotation over the start point but as a continuous annotation.
• Alignments: The performance of the algorithm for running multiple alignments has been improved and now runs on multiple cores.
• Find Open Reading Frames can be run in batch and workflows
• Translate to protein can be run in batch and workflows
• Restriction map: Excel export now creates a sheet for both the cut sites table and the restriction map.
• Alignments can be used as input for finding primer binding sites.
• Export now has progress and can be canceled.
• BLAST results and 3D structures can be exported as text.
• Batching: Previously, results where saved in the same folder as the input data. This can now be changed and a new save folder can be specified. Sub-folders will be created for each batch unit.
• The limit for the cloning editor has been increased to 6,000,000 bases (from 4,000,000 bases).
• Create Expression Clone (LR) from Gateway Cloning produces sequence object rather than a list
• Shortcut key for Translate to Protein has changed from Ctrl + Shift + T into Ctrl + Shift + P.

  Bug fixes

  • Fix to the proxy settings recognition meaning that Download of BLAST databases now work when there is a proxy setup.
  • Fixed problem of not correctly formatting qualifiers in EMBL export.
  • Fixed a problem sorting sequence lists on modification date.
  • Test on proportions: Fixed an error caused by the wrong group being used as reference, which means that the positive values should have been negative and vice versa.
  • Various bug fixes.

Bug fixes

• Fix to the proxy settings recognition meaning that download of BLAST databases now works when there is a proxy setup.
• Fixed problem of not correctly formatting qualifiers in EMBL export.
• Fixed a problem sorting sequence lists on modification date.
• Test on proportions: Fixed an error caused by the wrong group being used as reference, which means that the positive values should have been negative and vice versa.
• Various bug fixes.

Bug fixes

• Fixed: Workflows would fail when intermediate results were empty (e.g. if no variants were found and a variant track was used for subsequent analysis).
• Various bug fixes

New features

Workflow

• Workflows can be built in the Workbench to combine various tools from the Toolbox into one analysis, connecting the output from one tool to the input from another
• In the first release, the gateway cloning tools are the only tools that can be incorporated into workflows.
• Workflows can be distributed and installed either in the Workbench or in the CLC Genomics Server
• The creator of the workflow can configure parameters for the workflow and these will be fixed when the workflow is distributed and installed
• The creator of the workflow decides which of the output from the tools that should be saved and which should be discarded
• Workflows can be run in batch, making it a powerful tool for crunching high numbers of samples through the same pipeline.

Plugin updates

Improvements

• Support for Mac OS X 10.8, Mountain Lion

Bug fixes

• Fixed: Problem with online BLAST at NCBI

Improvements

• Aligned fasta import and export is now supported (see http://www.bioperl.org/wiki/FASTA_multiple_alignment_format). A consequence of this is that the standard fasta import of sequences will reject to import sequences that contain gaps, assuming they should be imported as alignments instead.
• The license order ID is visible in the License Manager, both for static and network licenses. For security reasons, the last 10 characters of the ID are masked. This will prevent unauthorized persons from copying the license order ID to another computer, but will allow the CLC staff to identify the license used.

Bug fixes

• Fixed: Cloning bug: when performing restriction cloning in regions with single-stranded DNA, you would get an error.

New features

New features

• Printing and pdf export of assemblies: the assemblies are now wrapped to make better use of the paper.
• Usability of Close icon on tabs has been improved. Both in terms of responsiveness and making it impossible by accident to initiate a drag and drop movement when you hit the close icon to try to close a tab.
• "Show" submenu has been removed from File Menu, and the right-click menu now includes only the relevant views and editors. This provides a better overview.
• The behavior of the Close Other Tabs function has changed so that it will close all views, regardless of the way the view area is split.
• The most common annotation types are assigned a special color per default. Other annotation types previously got the same color. This has been extended so that the Workbench attempts to find a special color for each type.
• VectorNTI import is no longer in a separate plug-in but part of the Workbench. The functionality remains unchanged.

New plug-ins and plug-in updates

• Additional Alignments Plug-in updated
  • The algorithms have been updated to the most recent versions
  • The list of algorithms has been reduced to two for compatibility reasons

New plug-ins and plug-in updates

• MLST module updated
  • Possible to download MLST schemes from any web site compatible with mlstDBnet
  • When a new allele is called because the sequencing reads are not long enough, this is reported in the isolate view rather than “New allele”

New and improved features

• Multi-site Gateway Cloning. You can perform multi-site gateway cloning and in a few clicks create your expression clones with multiple fragments. The existing Gateway Cloning tool has been expanded so that you can easily recombine several fragments as well as continue using it for the standard Gateway Cloning
• Process tagged sequences
  • A summary report is now available with an overview of the number of reads per bar code
  • You can search for barcodes (MIDs) on both strands, supporting new 454 protocol
• Find Binding Sites and Create Fragments improved:
  • If your template sequence contains ambiguity nucleotides (like N, Y etc), these will no longer count as mismatches when checking your primers. Note that the primer base of course need to be covered by the ambiguity symbol (e.g. a T would still be a mismatch if the template sequence has an R, which means either A or G)
  • Fixed: When using multiple template sequences, the choices to open or annotate a fragment from the fragment table did not work properly. They always applied to the first sequence although the fragment was located on another sequence (as indicated in the table)
• Exporting fastq format no longer includes redundant name of the read in the quality score line. Now the name only appears once per read

Bug fixes

• Fixed: Annotations spanning the sequence from start to end did not display right when the sequence was wrapped. The annotation was only displayed on the first line
• Fixed: Set-up experiment would crash when using many samples
• Fixed: Calculation of consensus sequence in read mappings: Sometimes a majority of gaps would be ignored and a base erroneously introduced in the consensus sequence. It occurs when 1) there is no coverage in an initial segment of the reference sequence, and 2) a gap is encountered in the global read alignment. From that point onwards, gap counts are included in the consensus vote, but they are taken from the start of the mapping (where they are all 0), so they are out of sync with associated base counts. High gap counts would then kick in further downstream, possibly making the consensus a gap where it should not be. We recommend checking your mapping results manually if you rely on using the consensus sequence for further analysis
• Fixed: importing adapters for trimming and barcodes for de-multiplexing did not work properly for CSV files and empty rows in Excel files were not allowed
• Fixed: Motif search did not exclude regions with Ns when the option “Exclude matches in N-regions for simple motifs” was selected

New and improved features

• You can switch between compactness levels by pressing the Alt key while scrolling with your mouse or touchpad
• Translation in the Side Panel of nucleotide sequences now includes options to translate “All forward” or “All reverse” reading frames
• Conflict table view of read mappings: reference positions also reported in addition to the consensus sequence position
• Alignments: it is now possible to copy all annotations from one sequence to other sequences in the alignment
• Cloning editor: number of restriction cut sites and motifs are shown separately for the sequence currently displayed and for all sequences in the list
• Restriction enzymes updated with latest REBASE version
• Clean-up of the Workbench window so that it no longer holds information about which Workspace is active. This information is now displayed with check boxes in the Workspace menu

Bug fixes

• Fixed: For circular molecules, the Find Open Reading Frames tool did not find reading frames on the negative strand. We recommend users to rerun any reading frame analyses on circular molecules
• Fixed: Experiments tables can now be exported in Excel and csv formats
• Fixed: BLAST searches at NCBI always searched nr or nt, regardless of which database was specified. This has been a problem since the release of CLC Main Workbench 6.0
• Fixed: Pattern discovery wizard failed when the tool is run for the second time
• Fixed: Certain annotation types were mapped to generic annotation types when exporting sequences in Genbank format

Bug fixes

• Fixed: A cache-related bug which would sometimes result in errors when running large jobs.
• Fixed: The UniProt search has been updated to reflect URL-changes at uniprot.org
• Fixed: A problem with microarray experiments where large experiments could not be analyzed

New and improved features

• All history entries will from now on include the version number of the software
• Performance of Excel 2010 exporter improved in terms of speed and memory requirements
• When using a license server, the Workbench user can now specify a custom user name which can be checked in the license server configuration. This makes it possible to get more fine-grained control of the users of the license server
• BLAST
  • BLAST parameters have been changed so that number of threads is 1 per default (there is a bug in the BLAST code provided by NCBI which makes it fails on certain data sets when using multiple threads)
  • The “Mask lower case” option has been removed
  • Tool to download BLAST databases from NCBI within the Workbench

Bug fixes

• Fixed: Alignment-based primer design failed for columns with many gaps
• Fixed: “Find Binding Sites and Create Fragments” did not find binding sites where the primer extended the 5′ end of the template sequence
• Fixed: Import of certain special Genbank files failed
• Various minor bug fixes

New and improved features

• Local BLAST is faster when blasting against small databases

Bug fixes

• Fixed: Local BLAST did not work on Mac OS 10.5
• Fixed: Joined annotations did not get the right off set when inserting a sequence in the cloning editor
• Fixed: Import of GO annotation files did not work
• Various minor bug fixes

Bug fixes

• Fixed issue with synonymous overhang characters in cloning editor
• Graphics export now works with restriction sites shown
• Gene Ontology Annotations can now be imported
• Improved support for Mac OS X systems with japanese language
• Improved support for systems with 512 MB of memory or less
• Blast: Fixed issue with BLAST database creation taking too long under certain circumstances
• Blast: Fixed issue concerning errors when input sequence names contained illegal characters
• Blast: Fixed issue with Extract And Open option being erroneously disabled
• Blast: Option to enter custom Entrez Query limits in Blast at NCBI re-introduced
• Blast: Improved speed when using Blast results as input to wizards

Improvements

• Cloning tool re-designed to make it easier and faster to perform restriction cloning
  • Restriction sites used to select target vector and fragment
  • Sequences can now be displayed in circular mode in the cloning editor
  • Only one sequence displayed at a time (there is a list at the top of the view to switch between sequences)
  • Option to clone several fragments and adjust overhangs and orientation in one dialog
  • New cloning tutorial available for a quick introduction
• BLAST tools have been redesigned
  • New Blast Database manager for easy administration and management of local BLAST databases
  • More user-friendly way of creating and accessing local BLAST databases
  • Much more stable design of both BLAST at NCBI and Local BLAST when running large data sets
  • The SNP Annotation using BLAST tool has been discontinued
  • See migration notes for using your old databases
• Improved layout of restriction site annotations
  • Linear view: There is a new option for displaying labels as “Stacked” which means that the labels of overlapping cut sites can be discriminated
  • Circular view: There is a “Radial” option that will place restriction sites (and annotations) as close to the sequence as possible with a radial layout
• Improved layout of general annotations
  • Linear view: There is an option to separate restriction sites and annotations in separate layers
  • Circular view: There is a “Radial” option that will place annotations (and restriction sites) as close to the sequence as possible with a radial layout
• Motif search available in Side Panel
  • Dynamic annotations will be added for motifs defined in the Side Panel (similar to restriction sites)
  • Use motif lists to add your own motifs to the Side Panel
• Annotation table now available for sequence lists, contigs, BLAST results and alignments
• Batching functionality available for selected tools
• Multiplexing: Process tagged sequencing data
  • It is now possible to import and use a file with bar codes and sample names. This makes it easier to process data with a high number of multiplexed samples
  • You can specify separate output folders for each sample, making it convenient to batch process the subsequent analyses
• Support for exporting tables as tab-delimited files
• Audit option: manual editing of sequences will be recorded with an annotation on the sequence (this has to be switched on in the Preferences dialog)
• The default database of restriction enzymes can be expanded (requires manual edit of database file)
• The default set of codon frequencies can be expanded (requires manual edit of table files)
• Improved option to export and import Side Panel settings
• Memory allocation: the default memory allocation for the Workbench changes from 75% to 50% of available physical memory with a maximum at 50 GB

Bug fixes

• The molecular weight calculation for the sequence statistics report is more accurate and is now reported for both single- and double-stranded molecules
• Various bug-fixes