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Tutorials

TutorialDownload
An Introduction to Workflows
Assemble Sequences to a Reference
Batching of Multi-Input Workflows
Bisulfite-Sequencing
BLAST Searches
ChIP Sequencing
ChIP Sequencing using Biomedical Genomics Workbench
Comparative analysis of three bovine genomes
Copy Number Variant Detection
De Novo Assembly and BLAST
De Novo Assembly of Paired Data
Dock Ligands from a 2D Sketch
Exploring Protein-Ligand Binding
Exploring your Protein
Expression Analysis with the Advanced RNA-Seq and Ingenuity Pathway Analysis Solution
Expression Analysis with the Advanced RNA-Seq Plugin
Find and Align Binding Pockets
Finding a Rare Disease Causing Variant
Folding RNA Molecules
Gateway Cloning
Genome Finishing Module – Using the Align Contigs Tool
Getting Started
Getting Started (Drug)
Identification of somatic variants in a matched tumor-normal pair
Identification of variants in a tumor sample
Microarray-based Expression Analysis
Microbiome Profiling using workflows
Modification of an existing workflow
Molecular Biology Basics
OTU Clustering and Analysis of Microbial Communities
Phylogenic Trees and Metadata
Read Mapping in Detail
Reference Genome and Annotations Tracks
Resequencing Analysis using Tracks
Resequencing – Map Reads to Reference and Variant Detection
RNA-Seq Analysis of Human Breast Cancer Data
Small RNA Analysis for Biomedical Genomics Workbench
Small RNA Analysis for Genomics Workbench
Typing and Epidemiological Clustering of Common Pathogens (beta)
Virtual Screening
Visualize variants on protein structure
Visualize variants on protein structure using the Biomedical Genomics workbench
Whole Metagenome Functional Analysis (beta)

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Data

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 (91.5 MB)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.
lumina/Solexa paired end genome data from E. coli commensal strain K-12 (168 MB)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.
AB/SOLiD genome data from Streptococcus suis (197 MB)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.
Illumina paired end genomic data from Pseudomonas aeruginosa (616 MB)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

CLC Formatted Data

Mapping data

NameDescriptionDownload
CLC formatted mapping data (19.2 MB)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

RNA-Seq data

NameDescriptionDownload
Subset of the full data set (12.9 MB)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
Experiments with the full data set (12.9 MB)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

Variant and protein structure data

NameDescriptionDownload
CLC formatted variant table and molecule project (0.8 MB)This data set contains 6 variants commonly found in the Bcr-Abl fusion gene, and used in the Biomedical Genomics Workbench and CLC Genomics Workbench tutorials.