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CLC Genomics Server early access 20.0

Release date: 2019-11-19

These are the draft release notes for CLC Genomics Server 20.0, due for release on December 11, 2019. The manual is available in PDF and HTML format. Installers for this product are available as "early access" via links at the bottom of this page. These products are not supported, and we recommend they are not used in production during the early access period. We recommend that the early access version is only installed if you have license covered by Maintenance, Upgrades and Support (MUS) dedicated for use on a test setup.

Server specific

New features

Workflows
  • A new workflow queuing option has been introduced and queuing option labels have been updated for clarity.
    • The new option, "Submit tasks in each workflow block to a single node" results in a CLC Grid Worker being launched for each iteration of a block and a CLC Grid Worker being launched for each additional block outside the iteration block(s). For workflows consisting of just one block, this option behaves just like the Submit all tasks to a single node option.
    • The option previously called "Classic" is now labeled "Submit individual tasks to any available node"
    • The option previously called "Single entity" is now labeled "Submit all tasks to a single node".
    • The section of the web administrative interface where these options appear, previously called "Job queuing options" has been renamed Workflow queuing options.

Improvements

External Applications
The administrative interface for External Applications has been reworked, providing better support for administration, configuration and collaborative development. Changes include:
  • The External applications tab of the web administrative interface groups configurations according to the subfolder of the Toolbox the external application is configured to appear under. For each configuration, version information, who last updated it and when is presented.
  • External applications can be dragged between the Toolbox folder groupings in the the web administrative interface, making it easy to put them into the appropriate subfolder as seen in the Workbench Toolbox. Configurations can also be dragged into the Drafts area, which changes the status of that configuration and makes it no longer available for use by client software.
  • The External Application configuration editor is now organized into tabs includes a new tab for options related to Management.
  • There is now a new Drafts area, for storing external application configurations that should not be available for use by client software. Previously, availability was managed using checkboxes beside each external application configuration name.
  • When an external application configuration is saved, just the configuration for that one application is updated. Previously, the save action would save all configurations.
  • A button for deleting external application configurations has been added, allowing individual or multiple external applications to be selected and then deleted in a single action. The option to create a backup copy is offered before the deletion is carried out.
General
  • The memory limit for CLC Grid Workers can be configured in grid presets via the web administrative interface.
  • There is finer control over the memory values that can be set when installing the CLC Genomics Server using the graphical installer.
  • Workflow logs now include information about tools in a workflow that failed to run to completion.
  • Copying files from a Workbench CLC_References location to the CLC Genomics Server CLC_References location is now faster.
  • Minor improvements to the organization of options under the Job distribution tab of the web administrative interface.
  • LDAP/AD groups containing illegal XML-1.0-characters (e.g. control-characters) are now omitted from the list of groups read from LDAP/AD. If this happens, error information is printed to the server log.
 

Bug fixes

  • Fixed a bug where every primary output from a workflow element was produced, even when output elements were not connected to them. This fix means that workflows now produce the same set of outputs, whether run on a CLC Server oer CLC Workbench.
  • Fixed a bug where Expression Browsers could not be exported if they contained GO annotation values with parentheses but no database reference.
  • Fixed an issue where the "Job category" setting in a grid preset was not sent to the underlying grid system.
  • Fixed an issue affecting external applications with parameters configured as "User selected files (Import/export directory)" with a default file specified. When such external applications are included in a workflow, a file specified in the workflow design, or, for unlocked parameters, a file selected when launching the workflow, will now take precedence over this default. Previously the file specified in the external application configuration was always used.
  • Fixed an issue where, when installing the software using the command line or setting the memory limit using a vmoptions file, the memory limit actually set was different than that specified. For most systems, this discrepancy is small relative to the amount of memory on the machine. (For example, on machine with 96Gb of memory, we expect the maximum discrepancy to be in the order of 2Gb.)

Changes

  • The previous default option in the Direct data transfer from client systems area, "Files uploaded via temporary file location on server system(s) (legacy)", has been retired. When upgrading on a system with that option selected, the new default, "Not allowed" is applied in the updated version. The option "Files uploaded via Import/Export location" must be selected to enable data transfer from client systems to your CLC Genomics Server. This option can be configured at any time and that configuration will be preserved when you upgrade. Please see the manual for further details, including what types of transfers are affected by this setting.
  • A new section called Cloud Settings is available under the Execution node settings of the web administrative interface. This section is present to support functionality associated with the Cloud Server Plugin, due for release early in 2020.

Shared with CLC Workbenches

New features

Workflows
  • NGS sequence data can be imported on the fly, as an initial action when a workflow is run, avoiding the need import the data prior to launching the workflow.
  • When launching workflows, batch units can now be defined using metadata, supplied either as a CLC medata table or by selecting an Excel format file containing information about the data.
  • Workflows with multiple inputs, where those inputs should be matched with each other, can now be launched in batch mode, making use of the ability to define batch units based on metadata. For example, a workflow where sets of reads should be mapped to different reference sequences can now be launched in batch mode.
  • Two new workflow elements have been introduced, Iterate and Collect and Distribute, which allow workflows to be designed where the execution of different parts of a workflow can be finely controlled. For example, using these elements, a single workflow can contain an RNA-Seq analysis step, typically run once per sample, as well as a Differential Expression for RNA-Seq step, typically run once for a set of samples. Similarly, a single workflow can be designed to run batches of trio analyses, producing cohort-level reports as outputs.
  • Workflows now produce a Workflow Result Metadata table, which contain one row per output, with the relevant data element associated with that row. When launched in batch mode, the batch the row relates to is clearly indicated.
Epigenomics analysis
  • Tools for detecting peaks in sequencing data are now available from a new 'Advanced Peak Shape Tools' folder found in the Epigenomics Analysis folder of the Toolbox:
  • A tool for detecting evidence for histone acetylation marks in genes or other predefined genomic regions is now in the Epigenomics Analysis folder of the Toolbox:
    • Histone ChIP-Seq This tool was formerly available via the Histone ChIP-Seq Server Plugin.
miRNA analysis (small RNA)
Import and export
  • Reports can now be exported in JSON format and in PDF format.
  • A new option in the Illumina importer, "Join reads from different lanes", will when enabled merge fastq files from the same sequencing run but from different lanes into a single sequences list.
  • Create Expression Browser can now use tables imported from CSV or Excel format files as an annotation resource. Using such tables, sort and filtering can be done according to numeric annotation values as well as textual annotations.
  • When exporting to PDF, there is now an option to export the history of the report.
Other new tools
  • Combine Reports Summarizes information from multiple reports and produces a single report. It can be used for combining different report types for a single sample, or combining reports for a set of samples.
  • Create Variant Track Statistics Report Creates a summary report for different types of variants in variant tracks.
RNA-seq Analysis
  • A new option, "Library type setting", in the RNA-Seq Analysis tool offers the selection of "Bulk", for analysis of samples where reads are expected to be uniformly distributed across the full length of transcripts , or "3' sequencing", which tailors the output and report quality control for samples generated using low input 3' sequencing applications. "Bulk" is the default, and corresponds to the behavior of the tool in previous software versions.
  • The definition of "Maximum number of hits for a read" in the RNA-Seq Analysis tool has been simplified. It now refers to the number of distinct places on the reference that a read maps best to. Previously, a more complex definition was used, involving checking for matches against genes and then against intergenic regions, with rules applied to the results.
  • The report generated by RNA-Seq Analysis now includes the percentage of reads mapped to transcripts of particular length ranges, aiding the interpretation of the "Coverage along normalized transcript length" graph.
Trim Reads
  • Sequences can now be trimmed to a fixed length from either the 3' or the 5' end.
  • New options have been added to allow homopolymer trimming to be finely tuned.
  • If "Trim ambiguous nucleotides" is enabled, ambiguous characters (e.g. N) at the end of sequences are removed, even if the number of these characters is lower than the limit set. Previously, such characters were left in place if their number was lower than the limit.
  • When included in a workflow, Trim Reads now always produces an output when an output element is connected to it. This includes the following situations:
    • Where no reads have been trimmed (either because all trimming options were deselected, or because none of the trim options matched any of the reads). In this case, the "Trimmed sequences" output will contain all input reads, "Discarded sequences" will be empty, and "Percentage trimmed" will be 100% in the report.
    • Where all reads have been trimmed. In this case, the "Discarded sequences" output will contain all input reads, "Trimmed sequences" will be empty, and "Percentage trimmed" will be 0%.
BLAST
  • A new option for the BLAST tool called Filter out redundant results, will when enabled cull HSPs on a per subject sequence basis by removing HSPs that are completely enveloped by another HSP.
  • The NCBI blast executables have been updated to version 2.9.0.
  • The option "Choose filter to mask low complexity regions" has been renamed to "Mask low complexity regions".
New options in analysis tools
  • A new option for Local Realignment called "Allow guidance insertion mismatches" allows reads to be realigned using guidance insertions that have mismatches relative to the read sequences. This option is enabled by default.
  • The creation of reads tracks (mappings) is now optional in the RNA-Seq Analysis tool.
  • A new option in Copy Number Variant Detection (CNVs) called "Merge overlapping targets" allows overlapping target regions to be merged into one larger target region. CNV calls are made on this larger region.
  • A new option called "Report unmethylated cytosines" is available for the Call Methylation Levels tool. When enabled, methylation levels are reported for all sites with read coverage, rather than only for sites with methylated cytosines.
  • Two new options in Create Mapping Graph are available for generating coverage tracks for reads that mapped best to a single location on the reference sequence: "Specific read coverage" and "Paired read specific coverage".

Improvements

Workflows
  • Placeholder-based naming of outputs in workflows can now be configured at a finer level: the {input} or {2} placeholder is now replaced by the name of the first workflow input by default. This can then be further configured to use the names of other inputs by specifying them by number after a colon in the placeholder. For example: {2:1,3} would be replaced by the names of workflow inputs number 1 and 3. Previously, a workflow output configured as {2} was replaced by a concatenation of all the workflow input names.
  • The "Export to PDF" tool can now be used in workflows to export reports in PDF format.
Performance improvements:
  • Mapping of NGS reads on multicore systems is now approximately 25% faster. Tools benefiting from this improvement include Map Reads to References, Map Reads to Contigs and Map Bisulfite Reads to Reference.
  • Saving analysis results to an SSD is now considerably faster.
  • The import of ZIP files has been improved: temporary objects are cleaned up during the import process, reducing the required disk space.
  • Moving and deleting many elements at once is now faster.
  • Emptying the Recycle bin now takes place in the background.
  • Basic Variant Detection, Fixed Ploidy Variant Detection, and Low Frequency Variant Detection have been optimized to work on machines with lower memory. The changes are most noticeable in situations where coverage is high or where many variants are called.
  • Improved memory handling when working with read mappings with very high coverage.
  • There are general performance improvements in the following areas:
    • BLAST and Add attB Sites tools when using large sequence lists
    • Making BLAST databases where most sequences have the same name.
Demultiplex Reads
  • Sequences with a single mismatch to a barcode and that can be grouped unambiguously can now be demultiplexed.
  • Demultiplex Reads is now multithreaded for faster execution.
  • The percentage or reads in each group is now reported to one decimal place in the report.
  • The percentage of reads not grouped is no longer included in the "Reads per barcode" plot in the report.
  • Various other minor improvements
QC reports
  • Plots in the "Per-base analysis" section of the graphical report produced by QC for Sequencing Reads no longer include a value for base position 0. Values at position 0 in these plots previously were not meaningful.
  • Base position numbering now starts with 1 in the coverage table of the supplementary report produced by the QC for Sequencing Reads tool. Previously the base position numbers started at 0.
  • The reports produced by the QC for Read Mapping and QC for Targeted Sequencing tools now also include the median coverage.
  • The coverage report generated by QC for Targeted Sequencing now includes the total length of target region positions with coverage below the specified level.
  • QC for Target Sequencing has been updated to:
    • Count circular reads (these were previously ignored)
    • Show relevant warning messages when the target region track contains regions that overlap or that cross the origin, both when the tool is ran, but also in the created report.
    • Report the correct number of mapped bases and specificity in Table 2.2, even when the target region track contains overlapping regions.
Import and export
  • When importing BED files using the Import Tracks tool, only the first three columns (chromosome, start and end positions) are now required to match UCSC specifications for the BED format. Remaining columns that do not match these requirements will be imported as Var1, Var2, etc.
  • The CSV importer has been updated:
    • Values no longer need to be enclosed in quotation marks in the CSV file to be successfully imported.
    • Data values starting with a numeric character but also containing non-numeric characters are now interpreted as text. Such values were previously converted to numbers and then only imported up to the first non-numeric character.
  • The import of Nexus files has been updated to more closely match the format specifications.
  • When selecting files to import from an import/export directory via a CLC Workbench, right-clicking on a folder name now brings up a menu with the options: "Add the content of a directory" or "Add the full content (recursively) of a directory".
  • The "Excel 2010" and "Excel 97-2007" exporters now export NaN and +/-Infinity values to #N/A.
  • When importing multiple files using the Standard Import, the process ends with an error if at least one of the files failed to import. The details of which file failed and why can be seen in the log.
  • The GenBank exporter now replaces any spaces in annotation names with underscores.
Metadata related
Create Box Plot
  • Create Box Plot now calculates the median and percentile values in the same way as the "quantile" method in R. This aligns with the way these values are calculated by other tools in the CLC Genomics Workbench.
  • Whiskers of boxplots now range from the lowest data point within 1.5 times the inter quartile range (IQR) of the lower quartile and the highest data point within 1.5 IQR of the upper quartile. Previously, they extended 1.5 times the length of the box (IQR).
Improvements to other analysis tools
  • The algorithm used to auto-detect paired distances when mapping NGS reads has been improved. Tools benefiting from this include Map Reads to References, RNA-Seq Analysis, Map Reads to Contigs and Map Bisulfite Reads to Reference.
  • Improvements to SRA download:
    • The temporary disk space needed to download data has been reduced significantly.
    • Technical reads are now discarded.
    • Orphan reads are now put into a separate output for paired data.
  • When importing multiple files containing sequencing reads (QIAGEN GeneReader, Illumina, PacBio, Fasta Read, Ion Torrent) or when importing SAM format files, a single problematic file does not stop the import. The import process now continues with the next file if it encounters a file that could not be imported.
  • The "Chromosome coverages" section in the results report produced by the "Copy Number Variant Detection (CNVs) tool" is now a table.
  • The "CPM" expression option in the side panel setting of the Expression Browser has been renamed "CPM (TMM-adjusted)" to reflect how it is calculated.
  • The TMM Normalization used in the Expression Browser, in Create Heat Map for RNA-Seq, PCA for RNA-Seq, Differential Expression in Two Groups, and Differential Expression for RNA-Seq, has been changed. The change involves how a reference column is selected for TMM Normalization, and is unlikely to lead to noticeable differences in results. Changes are most likely to occur in situations where the majority of transcripts/genes have zero expression.
  • The "All group pairs" and "Across groups (ANOVA-like)" comparisons in Differential Expression for RNA-Seq now compare expressions in the same direction. Previously, the fold changes reported by these 2 tests for the same data, entered in an identical order, had opposite signs.
  • The long form of the HGVS nomenclature for DNA is now used by the Amino Acid Changes tool for annotating coding region changes: the bases of deletions and duplications not longer than 50 nucleotides are included, and repeated sequences are reported using the insertion form.
  • Exon information added by Annotate with Exon Numbers now includes a blank entry if a variant is located in an intronic region. For locations with multiple isoforms annotated, this gives a one to one relationship between the number of exon annotations and the number of isoforms.
  • InDels and Structural Variants now consistently assigns a count of 1 for a paired read, leading to improved statistics. Previously, regions where the R1 and R2 reads overlapped were assigned a count of 2.
  • Filter Variants on Custom Criteria now prints a message to the log if any columns specified in the criteria are not present in the data.
  • The QC for Targeted Sequencing tool now sets the direction of each read in a pair independently, which can lead to more accurate forward and reverse coverage values in some situations.
  • Identify Shared Variants now reports homozygous sample frequency, heterozygous sample frequency and mean allele frequency.
Other improvements
  • Outputs of tools provided by plugins now include the plugin name and version in the element history.
  • Tool and workflow logs now include an "Elapsed time" column.
  • CLC URLs have been made more compact.

Bug fixes

  • Fixed a rare issue that could cause some jobs to fail when multiple instances of Filter Variants on Custom Criteria were run simultaneously.
  • Fixed a bug where failing import of Illumina .fastq files could leave files in the temporary files directory.
  • Fixed an issue in the "Duplicated sequences" section of the QC for Sequencing Reads graphical report, where the relative sequence count for the duplicate count of 100 was incorrectly reported in the field for the duplicate count of 99.
  • Fixed a bug where Expression Browsers could not be exported if they contained GO annotation values that included parentheses but no database reference.
  • Fixed an issue where moving a folder within a server location occasionally caused the contents of the folder to become corrupt, until the persistence was reindexed.
  • Fixed an issue in RNA-Seq Analysis where an error message was produced if the value entered for "Minimum read count fusion gene table" was 1 and no fusions were found.
  • Fixed an issue in Copy Number Variant Detection (CNVs) algorithm reports, where values in the "Start BIC" and "End BIC" columns in section 3.1 were truncated to a maximum of 4 digits in the integer part. The underlying calculations were not affected.
  • Fixed an issue where the Gene Set Test tool did not exclude relevant GO terms as computationally inferred if there were parentheses in the GO annotation description.
  • Fixed an issue in the Basic Variant Detection, Fixed Ploidy Variant Detection and Low Frequency Variant Detection tools that in rare cases could result in the QUAL value reported being slightly different between runs.
  • Fixed an issue in Basic Variant Detection, Fixed Ploidy Variant Detection and Low Frequency Variant Detection where the tool could continue to use the CPU and write to disk even after a job was cancelled.
  • Fixed an issue in the GFF2 importer with different representation of stop codons in the CDS regions due to differences in input formats.
  • Fixed an issue in Map Reads to Reference where the summary statistics table in the report did not include paired read statistics for mappings with paired end reads if no reads were mapped in intact pairs.
  • Various minor bugfixes

Changes

  • The Java version bundled with CLC Genomics Server 20.0 is Java 11, where we use the JRE from AdoptOpenJDK.
  • On Linux systems, the 'fontconfig' software package and at least one font package (e.g dejavu-sans-font) are required as the Java JRE no longer includes default fonts. The Linux installer for the CLC Genomics Server no longer includes the 'fontconfig' package, which must therefore be installed separately before running the CLC Genomics Server installer. The CLC Genomics Server installer will verify during installation if the required package(s) for font handling are installed. If the font handling packages are missing, the installer will exit with the following message:ERROR: Required package 'fontconfig' not found. Please make sure fontconfig is installed together with at least one font package (for example dejavu-sans-font). Aborting ...
  • The {input} or {2} placeholder used when naming outputs from workflows is now replaced by the name of the first workflow input by default. Previously, it was replaced by a concatenation of all the workflow input names.
  • The tool Remove Orphan Reference Variants is now called Remove Homozygous Reference Variants.
  • The naming of some outputs from some tools have been updated:
    • Demultiplex Reads
      • Grouped reads Now: <sample name> <Barcode name> Previously: <Barcode name>
      • Ungrouped reasds Now: <sample name> Not grouped Previously: Not grouped
      • Report Now: <sample name> Demultiplex Reads report Previously: Demultiplex Reads report
      • Where multiple sequence lists are provided as input, the name of the first selected sample is used as the sample name.
    • Trim Reads
      • Trimmed, paired sequences Now: <sample name> (paired, trimmed pairs) Previously: <sample name> (paired) trimmed (paired)
      • Trimmed, broken pairs Now: <sample name> (paired, trimmed orphans) Previously: <sample name> (paired, trimmed orphans)
      • Discarded sequences Now: <sample name> (discarded) Previously: <sample name> (discarded)
      • Report Now: <sample name> report Previously: <sample name>(trim report)
      • In the case where multiple sequence lists were provided as input to the Trim Reads, the name of the first selected sample will be used in the output.
    • RNA-Seq analysis tool and Map Reads to Reference
      • Output names have been shortened: the content of the last set of parentheses of the input name is replaced by in the output name with a new tag denoting the specific type of output. Previously, tags were added to the input names when forming the output name.
      • The word "un-mapped" has been replaced with "unmapped" in output names.
      • When unmapped reads outputs are added to metadata tables the inputs are associated with, they are are now assigned the metadata role "Unmapped reads".
  • The following are legacy tools. "(legacy") has been appended to their names and they will be removed in a future version of the software.
    • Create Combined RNA-Seq Report: The new "Combine Reports" tool includes this functionality, and should be used to combine RNA-Seq reports.
    • Create Track from Experiment
    • Reverse Sequence
    • Small RNA Analysis
    • Extract and Count
    • Download miRBase
    • Annotate and Merge Counts
    • Remove Reference Variants The functionality of this tool can be replicated using "Filter Variants on Custom Criteria" with relevant criteria. To remove reference variants where the alternate allele has already been filtered away, use the new tool Remove Homozygous Reference Variants.

Functionality retirement

The following tools have been retired:
  • Identify Differentially Expressed Gene Groups and Pathways (legacy)
  • Add Fold Changes (legacy)
  • Add Information from Overlapping Genes (legacy)
  • Create Fold Change Track (legacy)
  • Download Reference Genome Data (legacy)
The import of the following formats is no longer supported:
  • qseq
  • scarf

Compatibility

The follow are the corresponding client applications for CLC Genomics Server 20.0
      • CLC Genomics Workbench 20.0
      • CLC Main Workbench 20.0
      • CLC Command Line Tools 20.0

Plugin notes

Plugin retirements

Functionality of the following plugins has been integrated into the CLC Genomics Server:
  • Histone CHIP-Seq Server Plugin
  • Advanced Peak Shape Tools Server Plugin

Advanced notice

The following tools will be removed in a future release of the software:
  • Create Combined RNA-Seq Report (legacy)
  • Create Track from Experiment (legacy)
  • Remove Reference Variants (legacy)
  • Reverse Sequence (legacy)
  • Roche 454 NGS import (legacy)
  • Extract and Count (legacy)
  • Download miRBase (legacy)
  • Annotate and Merge Counts (legacy)
The "Run in Batch Mode" functionality used for launching workflows with multiple inputs from a CLC Workbench is now legacy. Such workflows can now be launched in batch mode from a CLC Workbench by checking the "Batch" checkbox when selecting the input data.   If you are concerned about these proposed changes, please contact our Support team by emailing [email protected].  

CLC Server Command Line Tools

Please see the CLC Genomics Server 20.0 listings above for the details about the new tools and features listed here. These are the draft release notes for CLC Server Command Line tools 20.0, due for release on December 11, 2019. The manual is available in PDF and HTML format. Installers for this product are available as "early access" via links at the bottom of this page. These products are not supported, and we recommend they are not used in production during the early access period. To download a commercial license for this product, you must have a license covered for Maintenance, Upgrades and Support (MUS). A 2 week evaluation license is available via the License Manager within the software.

New tools

Epigenomics analysis
Tools for detecting peaks in sequencing data are now available and can be called using the following commands:
  • peak_shape_apply_filter Apply Peak Shape Filter
  • peak_shape_learn_filter Learn Peak Shape Filter
  • peak_shape_score_regions Score Regions
  • histone_chip_seq Histone ChIP-Seq
The first three of these commands were formerly available via the Advanced Peak Shape Tools Server Plugin (beta), and the fourth via the Histone ChIP-Seq Server Plugin.
miRNA analysis (small RNA)
Tools for analyzing miRNA data are now available and can be called using the following commands:
  • create_combined_mirna_report Create Combined miRNA Report
  • ann_w_rna_central_accession_numbers Annotate with RNAcentral Accession Numbers
  • quantify_small_rna Quantify miRNA
These commands were formerly available via the Biomedical Genomics Analysis Server Plugin.
Import and export
  • export_pdf Export report to PDF format
  • export_report_json Export report to JSON format
Other new tools
  • combine_reports Combine Reports
  • variant_statistics_report Create Variant Track Statistics Report

New features for existing tools

  • trim - new options added
    • --fixed-length-trimming-end
    • --fixed-length-trimming-max-length
    • --fixed-length-trimming-trim
    • --poly-a-trim
    • --poly-c-trim
    • --poly-g-trim
    • --poly-t-trim
    • --trim-3-prime
    • --trim-5-prime
  • ngs_import_illumina - new option added
    • --join-lanes
  • rna_seq - new options added
    • --create-reads-track
    • --library-type
  • cnv_detection - new option added
    • --merge-overlapping-targets
  • mapping_graph_tracks
    • --paired-end-specific-coverage
    • --single-match-coverage
  • blast - new options added
    • --blastn-use-best-hit
    • --blastp-use-best-hit
    • --blastx-use-best-hit
    • --tblastn-use-best-hit
    • --tblastx-use-best-hit

Changes

  • The Java version bundled with the <product name> has been updated to the Java 11, where we now use the JRE from AdoptOpenJDK.
  • remove_orphan_reference_variants should now be called using remove_homozygous_reference_variants.
  • A new option, -L, has been added to support functionality associated with the Cloud Server Plugin, due for release early in 2020.
Commands changed
  • ngs_import_iontorrent Removed options: --linker-sequence, --max-distance, --max-distance, --min-distance, --paired-reads, --read-orientation
  • ngs_import_genereader Removed options: --discard-failed-reads, --illumina-trim, --max-distance, --miseq-demultiplexing, --paired-reads, --quality-score, --read-orientation
Commands removed
  • add_fold_changes_to_variant
  • add_info_overlapping_genes
  • create_fc_from_expr_tracks_algo
  • download_genome
  • go_analysis_expression_change
 

Advanced Notice

  • The remove_orphan_reference_variants command will be retired in a future version of the product. The remove_homozygous_reference_variants command runs the same tool, but using a new name.
If you are concerned about these proposed changes, please contact our Support team by emailing [email protected].  

Early Access installers for CLC Genomics Server and CLC Server Command Line Tools

These products are not supported, and we recommend they are not used in production during the early access period.