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Workbench plugins

PluginManualSupported onDownloadDeveloper

Additional Alignments

Perform alignments with ClustalO, ClustalW and MUSCLE

CLC Sequence Viewer CLC Main Workbench CLC Cancer Research Workbench CLC Drug Discovery Workbench CLC Genomics Workbench

Advanced Peak Shape Tools Plugin

Peak finding using shape information

CLC Cancer Research Workbench CLC Genomics Workbench

Annotate with GFF file

Using this plug-in it is possible to annotate a sequence from list of annotations found in a GFF file
Located in the Toolbox.

CLC Main Workbench CLC Cancer Research Workbench CLC Genomics Workbench

Batch Rename

Rename files in batch by adding a prefix or a number.

CLC Sequence Viewer CLC Main Workbench CLC Cancer Research Workbench CLC Drug Discovery Workbench CLC Genomics Workbench

Biobase Genome Trax Annotate

Create tracks with various data from Biobase Genome Trax

CLC Cancer Research Workbench CLC Genomics Workbench

Biobase Genome Trax Download

Create tracks with various data from Biobase Genome Trax

CLC Cancer Research Workbench CLC Genomics Workbench

Blast2GO PRO

Blast2GO PRO is an all-in-one tool for functional annotation of (novel) sequences and the analysis of annotation data.

CLC Main Workbench CLC Cancer Research Workbench CLC Genomics Workbench

Blast2GO Viewer

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

CLC Main Workbench CLC Cancer Research Workbench CLC Genomics Workbench

Bookmark Navigator

With this extension you can bookmark elements in the Navigation Area.

CLC Sequence Viewer CLC Main Workbench CLC Cancer Research Workbench CLC Drug Discovery Workbench CLC Genomics Workbench

CLC MLST Module

MLST Module makes it easy and fast to do MultiLocus Sequence Typing.

CLC Main Workbench CLC Cancer Research Workbench CLC Genomics Workbench

CLC Microbial Genome Finishing Module

Various tools for genome finishing aimed to close and produce high quality genomes in sequencing projects.

CLC Cancer Research Workbench CLC Genomics Workbench

CLC Workbench Client Plugin

Client plugin for connecting to a CLC Genomics Server, CLC Drug Discovery Server or Bioinformatics Database. The plug-in also includes Grid Engine Integration.

CLC Main Workbench CLC Cancer Research Workbench CLC Drug Discovery Workbench CLC Genomics Workbench

Copy Number Variant Detection

Detects copy number variations

CLC Cancer Research Workbench

Cytognomix Dependencies HG18

Dependencies required by the Shannon human splicing pipeline (NCBI36/hg18)

CLC Cancer Research Workbench CLC Genomics Workbench

Cytognomix Dependencies HG19

Dependencies required by the Shannon human splicing pipeline (GRCh37/hg19)

CLC Cancer Research Workbench CLC Genomics Workbench

Cytognomix Shannon Pipeline

Shannon human splicing pipeline for use in a CLC Genomics Workbench

CLC Cancer Research Workbench CLC Genomics Workbench

Cytognomix Shannon Pipeline Client

Shannon human splicing pipeline for use in a CLC Genomics Workbench

CLC Cancer Research Workbench CLC Genomics Workbench

Duplicate Mapped Reads Removal

Remove duplicate reads from mapping data.

CLC Cancer Research Workbench CLC Genomics Workbench

Duplicate Reads Removal

Detects and removes duplicate reads

CLC Cancer Research Workbench CLC Genomics Workbench

External Applications Client Plugin

Run external applications on a CLC Server via the Workbench menu system. External applications are made available by a Server admin configuring them in the CLC Server web interface.

CLC Main Workbench CLC Cancer Research Workbench CLC Drug Discovery Workbench CLC Genomics Workbench

Ingenuity Pathway Analysis

Ingenuity Pathway Analysis plug-in

CLC Cancer Research Workbench CLC Genomics Workbench

Ingenuity Variant Analysis Trial

Test Ingenuity Variant Analysis. Upload your variants to Ingenuity Variant Analysis and have a look at the result for a limited time.

CLC Cancer Research Workbench

KLAST Plugin (12 cores)

KLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of the Blast suite of algorithms. Relying on unique software architecture, KLAST takes full advantage of recent multi-core personal computers without requiring any additional hardware devices.

CLC Main Workbench CLC Cancer Research Workbench CLC Genomics Workbench

KLAST Plugin (4 cores)

KLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of the Blast suite of algorithms. Relying on unique software architecture, KLAST takes full advantage of recent multi-core personal computers without requiring any additional hardware devices.

CLC Main Workbench CLC Cancer Research Workbench CLC Genomics Workbench

KLAST Plugin (8 cores)

KLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of the Blast suite of algorithms. Relying on unique software architecture, KLAST takes full advantage of recent multi-core personal computers without requiring any additional hardware devices.

CLC Main Workbench CLC Cancer Research Workbench CLC Genomics Workbench

Metadata Import

Import metadata from a tabular file, or associate data already imported with metadata from a tabular file.

CLC Main Workbench CLC Cancer Research Workbench CLC Genomics Workbench

PPfold

Parallel pfold implementation

CLC Sequence Viewer CLC Main Workbench CLC Cancer Research Workbench CLC Drug Discovery Workbench CLC Genomics Workbench

Paracel BLAST Evaluation

Paracel BLAST Evaluation

CLC Main Workbench CLC Cancer Research Workbench CLC Drug Discovery Workbench CLC Genomics Workbench

QIAGEN GeneRead Panel Analysis Plugin

The QIAGEN GeneRead panel analysis plugin

CLC Cancer Research Workbench

RNA-Seq Legacy

Legacy version of the RNA-seq algorithm.

CLC Cancer Research Workbench CLC Genomics Workbench

Rapid Neighbour-Joining

A fast and memory efficient implementation of the Neighbour-Joining method with fast distance estimation.

CLC Sequence Viewer CLC Main Workbench CLC Cancer Research Workbench CLC Drug Discovery Workbench CLC Genomics Workbench

Read Mapping Legacy

Legacy version of the QIAGEN Aarhus Read Mapper algorithm

CLC Cancer Research Workbench CLC Genomics Workbench

Recent Items Navigator

With this extension you can keep track of recently used items in the Navigator Area.

CLC Sequence Viewer CLC Main Workbench CLC Cancer Research Workbench CLC Drug Discovery Workbench CLC Genomics Workbench

Sequence Reader

The sequence reader can be used to read aloud a part of a sequence.

CLC Main Workbench CLC Cancer Research Workbench CLC Genomics Workbench

SignalP

Integrated signal peptide prediction using SignalP 4.1 at http://www.cbs.dtu.dk/services/SignalP.
(Requires an Internet connection).

CLC Main Workbench CLC Cancer Research Workbench CLC Drug Discovery Workbench CLC Genomics Workbench

TMHMM

Integrated transmembrane helix prediction using TMHMM at http://www.cbs.dtu.dk/services/TMHMM.
(Requires an Internet connection).

CLC Main Workbench CLC Cancer Research Workbench CLC Drug Discovery Workbench CLC Genomics Workbench

TRANSFAC TFBS

The TRANSFAC TFBS extension can be used to search for putative transcription factor binding sites in DNA sequences. This release is based on the 2014.4 release of the Biobase TRANSFAC matrix profiles.

CLC Main Workbench CLC Cancer Research Workbench CLC Genomics Workbench

Transcript Discovery

The transcript discovery plug-in enables you to map RNA-Seq reads to a genomic reference and predicts transcripts and genes.

CLC Cancer Research Workbench CLC Genomics Workbench

Transfac (Free)

The TRANSFAC extension can be used to search for putative transcription factor binding sites in DNA sequences.

CLC Main Workbench CLC Cancer Research Workbench CLC Genomics Workbench

Vector NTI import

Vector NTI data import functionality.

CLC Sequence Viewer CLC Main Workbench CLC Cancer Research Workbench CLC Drug Discovery Workbench CLC Genomics Workbench

Server plugins

PluginManualSupported onDownloadDeveloper

Additional Alignments Server Plugin

Perform alignments with ClustalO, ClustalW and MUSCLE

CLC Cancer Research Server Solution CLC Genomics Server CLC Science Server

Advanced Peak Shape Tools Server Plugin

Peak finding using shape information

CLC Cancer Research Server Solution CLC Genomics Server

Annotate with GFF file server plugin

Using this plug-in it is possible to annotate a sequence from list of annotations found in a GFF file

CLC Cancer Research Server Solution CLC Genomics Server CLC Science Server

Biobase GenomeTrax Server Plugin

Biobase GenomeTrax Server Plugin

CLC Cancer Research Server Solution CLC Genomics Server

Convert Variant Tracks Server Plugin

This plugin lets you convert old variations tracks to new variant tracks.

CLC Genomics Server CLC Cancer Research Server Solution

Copy Number Variant Detection Server

Detects copy number variations

CLC Cancer Research Server Solution

Cytognomix Shannon Pipeline Server

Shannon human splicing pipeline for use on a CLC Genomics Server

CLC Cancer Research Server Solution CLC Genomics Server

Duplicate Mapped Reads Removal Server Plugin

Duplicate Mapped Reads Removal

CLC Cancer Research Server Solution CLC Genomics Server

Duplicate Reads Removal Server Plugin

Detects and removes duplicate reads

CLC Cancer Research Server Solution CLC Genomics Server

Ingenuity Pathway Analysis Server Plugin

Ingenuity Pathway Analysis Server Plug-in

CLC Cancer Research Server Solution CLC Genomics Server

Ingenuity Variant Analysis Server Plugin

Ingenuity Variant Analysis Server plug-in

CLC Cancer Research Server Solution CLC Genomics Server

Map Reads to Reference Affine Server Plugin

A fast and memory efficient read mapper with affine gap cost

CLC Genomics Server CLC Cancer Research Server Solution

Paracel BLAST Server

Paracel BLAST Server

CLC Cancer Research Server Solution CLC Genomics Server

QIAGEN GeneRead Panel Analysis Server Plugin

The QIAGEN GeneRead panel analysis server plugin

CLC Cancer Research Server Solution

RNA-Seq Legacy Server Plugin

Legacy version of the RNA-seq algorithm.

CLC Cancer Research Server Solution CLC Genomics Server

Read Mapping Legacy Server Plugin

CLC Cancer Research Server Solution CLC Genomics Server

Transcript Discovery Server Plugin

The transcript discovery plug-in enables you to map RNA-Seq reads to a genomic reference and predicts transcripts and genes.

CLC Cancer Research Server Solution CLC Genomics Server

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