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CLC Assembly CellPDFOnline
CLC Bioinformatics CellPDFOnline
CLC Bioinformatics Database (Administrator)PDFOnline
CLC Bioinformatics Database (End user)PDFOnline
CLC Bioinformatics Database ToolPDFOnline
CLC Genomics Server (Administrator)PDFOnline
CLC Genomics Server (End user)PDFOnline
CLC Genomics Server with database (Administrator)PDFOnline
CLC Genomics Server with database (End user)PDFOnline
CLC Genomics WorkbenchPDFOnline
CLC License ServerPDFOnline
CLC Main WorkbenchPDFOnline
CLC Science Server (Administrator)PDFOnline
CLC Science Server (End user)PDFOnline
CLC Science Server with database (Administrator)PDFOnline
CLC Science Server with database (End user)PDFOnline
CLC Sequence ViewerPDFOnline
CLC Server Command Line ToolsPDFOnline
Molegro Data ModellerPDFOnline
Molegro Molecular ViewerPDFOnline
Molegro Virtual DockerPDFOnline

Plugins

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Additional alignment pluginPDFOnline
Annotate Sequence with GFF FilePDFOnline
Batch renamePDFOnline
Biobase Genome Trax AnnotatePDFOnline
Biobase Genome Trax DownloadPDFOnline
BIOBASE TRANSFACPDFOnline
Blast2GO PROPDFOnline
Bootstrapped ROC (bROC)PDFOnline
Duplicate mapped reads removal pluginPDFOnline
Duplicate reads removal pluginPDFOnline
Extract annotationsPDFOnline
Ingenuity integrationPDFOnline
Local Realignment PluginPDFOnline
MedQL Variant PrioritizerPDFOnline
MedQL Variant Prioritizer (Free Version)PDFOnline
Metadata Import PluginPDFOnline
Microbial Genome Finishing ModulePDFOnline
MLSTPDFOnline
Omixon PreciseAlignPDFOnline
Paracel BLASTPDFOnline
Paracel BLAST EvaluationPDFOnline
PPfold Plug-inPDFOnline
Recent itemsPDFOnline
Sequence readerPDFOnline
Shannon Human Splicing PipelinePDFOnline
Shannon Human Splicing Pipeline ClientPDFOnline
Structural variationPDFOnline
Transcript discoveryPDFOnline

Deployment

ManualDownloadRead
CLC Deployment ManualPDF Online

Example Data

Next Generation Sequencing example data

Import the example data into CLC Genomics Workbench:

  • Download and save the relevant data set below
  • Unless otherwise stated, unzip the file
  • Open CLC Genomics Workbench
  • Click File->Import
  • Select the appropriate NGS format to start up the appopriate Import wizard

Raw Data

NameDescriptionDownload
Roche/454 pyrosequencing genome data from E. coli commensal strain K-12 The data set contains three files:
  • Ecoli.FLX.fna - FASTA file of the individual sequence reads from the E. coli K-12 genome
  • Ecoli.FLX.qual - Corresponding quality score values for each base in the sequence reads. Quality scores indicate the probability that an individual called base is correct in the sequence.
  • E. coli K-12 genome - A genome reference sequence of the E. coli K-12 genome is provided for read mapping.
 Download
lumina/Solexa paired end genome data from E. coli commensal strain K-12 The data set contains three files:
  • s_1_1_sequence.txt - FASTQ file containing sequence data and quality scores of the FIRST paired end reads from the E. coli K-12 genome
  • s_1_2_sequence.txt - FASTQ file containing sequence data and quality scores of the SECOND paired end reads from the E. coli K-12 genome
  • E. coli K-12 genome - A genome reference sequence of the E. coli K-12 genome is provided for read mapping.
 Download
AB/SOLiD genome data from Streptococcus suis The data set contains three files:
  • GRACE20070409_Suis-frag-20070425_F3_sequence.csfasta - COLORSPACE-FASTA file containing sequence data from the Streptococcus suis genome
  • GRACE20070409_Suis-frag-20070425_F3_sequence.QV.qual - Corresponding quality score values for each base in the sequence reads. Quality scores indicate the probability that an individual called base is correct in the sequence.
  • Streptococcus suis genome - A genome reference sequence of the Streptococcus suis genome is provided for read mapping.
 Download
Illumina paired end genomic data from Pseudomonas aeruginosa The data set contains four files:
  • SRR396637.sra_1.fastq and SRR396637.sra_2.fastq - paird end (FR) sequence reads. A distance range 150 to 350 is reasonable
  • SRR396636.sra_1.fastq and SRR396636.sra_2.fastq - mate pair (RF) sequence reads. A distance range 2000 to 3800 is reasonable
This data set is used in the De novo analysis of paired data tutorial 		Download
Small RNA data (SRR038853) from the MELB sample (a primary melanocyte cell) from GEO Sample GSM458536 The data set contains one file:
  • sra_data.fastq.gz - a compressed file containing fastq formatted sequence reads
This data can be imported directly using the Illumina importer. There is no need to de-compress this file before import
This dataset is used in the Small RNA Analysis tutorial 		Download

CLC Formatted Data

Mapping data

NameDescriptionDownload
CLC formatted mapping data This data set contains genomic sequencing reads from a cancer sample and a normal sample for the human mitochondrial genome.
Also included in the dataset is the chromosome M sequence from the hg18 build of the human genome as well as annotation tracks generated from data from UCSC Genome Browser site.
This dataset does not need to be uncompressed before import. Use the Standard Import option to import the whole file.
Instructions on importing this data and using it are included in the Resequencing and Tracks tutorial. 		Download

RNA-Seq data

NameDescriptionDownload
Subset of the full data set This data set is based on the data set published with [Mortazavi et al., 2008]. Includes a subset of the full data set including a region of chromosome 16 for use as a reference. Read introduction and instruction on how to use the data set Download
Experiments with the full data set This data set is based on the data set published with [Mortazavi et al., 2008] Includes experiments containing the expression values for the full data set. Read introduction and instruction on how to use the data set Download

PFAM database:

NameDescriptionDownload
PFAM (4 MB database) Top 100 occuring protein domains Download
PFAM (21 MB database) Top 500 occuring protein domains Download
PFAM (353 MB database) Complete Database Download