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Plugin made by CLC bio  
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Additional Alignment

This extension allows for use of two other alignment methods which are otherwise not distributed with CLC Workbench.

Annotate Sequence with GFF File

The Annotate Sequence with GFF File makes it very easy to annotate a sequence with annotations from a GFF file (Generic Feature Format).

Batch Rename

Rename sequences and other kinds of data in a batch. Either by adding text to the name, replacing existing text or by enumerating the data.

Biobase Genome Trax Annotate

The purpose of the Biobase Genome Trax plugin is to provide direct access to Biobase's Genome Trax from CLC Genomics Workbench.

Biobase Genome Trax Download

The purpose of the Biobase Genome Trax Download plug-in is to provide direct access to Biobase's Genome Trax from CLC Genomics Workbench.

BIOBASE TRANSFAC

The TRANSFAC extension can be used to search for putative transcription factor binding sites in DNA sequences. The binding site predictions are done by the Match tool, which uses the positional weight matrix library from TRANSFAC to analyze your sequences.

Blast2GO PRO

Blast2GO PRO is a methodology for the functional annotation and analysis of gene or protein sequences

Blast2GO Viewer

Blast2GO Viewer is a free plug-in to view Blast2GO project file generated with the commercial Blast2GO PRO plug-in.

Bookmarks

The bookmarks extension can be used to bookmark elements in the Navigation Area so that they can easily be found later on. This is particularly helpful if you have some data that you use in several different projects.

Bootstrapped ROC (bROC)

bROC algorithm is used in the discovery of differentially expressed probes/genes in microarray and RNA-seq experiments.

CLC Workbench Client plugin

Plugin for connecting your workbench to a server.

Combined Variant Caller

The Combined Variant Caller Plugin is required if you wish to use a CLC Genomics Server together with a CLC Cancer Research Workbench.

Convert Variant Tracks

As of Genomics Workbench 6.5 variant tracks has changed type.

Cytognomix Dependencies HG18

Dependencies required by the Shannon human splicing pipeline.

Cytognomix Dependencies HG19

Dependencies required by the Shannon human splicing pipeline.

Ingenuity Integration

The Ingenuity integration plug-in allows you to uploads genes and expression data directly from the CLC bio analysis to the Ingenuity Pathway Analysis (IPA) tools for downstream biological interpretation.

KLAST on 12 computer cores

KLAST is a high-performance sequence similarity search tool.

KLAST on 4 computer cores

KLAST is a high-performance sequence similarity search tool.

KLAST on 8 computer cores

KLAST is a high-performance sequence similarity search tool.

Microbial Genome Finishing Module

CLC Microbial Genome Finishing Module is designed for finishing of bacterial genomes or genomes of similar size. The module contains a range of tools designed to automate steps in the finishing process, help organise contigs and solve problems in assemblies. The module is an add-on to CLC Genomics Workbench.

MLST Module

MLST is a software module for Multilocus Sequence Typing (MLST). MLST is a portable and precise state-of-the-art technique for typing bacteria and yeast isolates.

Paracel BLAST

Paracel BLAST improves the normal performance of BLAST by distributing its execution to a cluster of PB worker nodes, thereby completing the search much faster.

Paracel BLAST Evaluation

The Paracel BLAST plugin integrates the command line tool Paracel Blast (PB) into the CLC Workbench.

PPfold

PPfold is a program to predict the consensus secondary structure of RNA alignments. It is a multithreaded and improved version of the popular pfold program.

Rapid Neighbour-Joining

Rapid Neighbour-Joining plugin is a very fast and scalable implementation of the canonical Neighbour Joining method by Saitou and Nei, which is a widely used method for building phylogenetic trees.

Read Mapper Legacy Version

This is the version of the read mapper that was used before Genomics Workbench 5.5. This plugin will be phased out in future versions of CLC Genomics Workbench.

Recent Items

The recent items navigator can be used to see the elements that you have recently opened or used.

RNA-Seq Analysis Legacy Version

This is the version of RNA-Seq Analysis used before CLC Genomics Workbench 7.0 and CLC Genomics Server 6.0. This version will be discontinued by end of 2014.

Sequence Reader

The sequence reader can be used to read aloud a part of a sequence. This is useful if you wish to compare a sequence on the screen to a printed sequence.

Shannon Human Splicing Pipeline

The splicing mutation pipeline plugin finds and interprets genomic variants that alter mRNA splicing in human exome, targeted sequencing, or complete genome data.

Shannon Human Splicing Pipeline Client

This plugin allows you to run the Shannon Human Splicing Pipeline on a CLC Genomics Server. It can not be used to perform the analysis locally in the CLC Genomics Workbench. If you need this functionality please download the commercial plugin called "Cytognomix Shannon Pipeline".

SignalP (Peptide prediction)

The Signal Peptide Prediction Plug-in can be used to find secretory signal peptides in protein sequences.

Transmembrane Helix Prediction

The Transmembrane helix prediction plugin can be used to predict transmembrane helices.

Plugin made by CLC bio  
Third party plugin

Beta

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Duplicate Mapped Reads Removal

The Duplicate Mapped Reads Removal plugin is designed to remove duplicate reads from mapping data.

Duplicate Reads Removal

The duplicate reads removal plug-in is designed to filter out duplicate reads. This tool is specifically well-suited to handle duplicate reads coming from PCR amplification errors which can have a negative effect because a certain sequence is represented in artificially high numbers.

Memory Efficient Read Mapper

A new read mapper for NGS reads with low memory requirements.

Metadata Import

The Metadata Import plug-in will allow you to associate metadata with your sequences and other data inside the Workbench.

Peak Shape ChIP-Seq

A beta version of the new ChIP-Seq analysis tool from CLC bio, using a method based on peak shape to accurately detect peaks in ChIP-Seq data.

Transcript Discovery

The Ab Initio Transcript discovery plugin is designed to discover transcripts by mapping RNA-Seq sequencing reads to a genomic reference, allowing large gaps (for introns), followed by a transcript discovery process where transcripts are inferred from the read mappings.