Product features

CLC Genomics Workbench includes all features of CLC Main Workbench and the following additional functionalities:

Genomics

Assembly view, zoomed to 100%, together with a conflict table view. A row in the table has been selected, and the associated conflict position is automatically highlighted in the assembly view.
Figure 1 (click to enlarge): Assembly view, zoomed to 100%, together with a conflict table view.
• De novo assembly of Sanger, 454, Illumina Genome Analyzer, and SOLiD data
• De novo assembly of mixed datasets (e.g. 454 and Illumina Genome Analyser)
• Contig report that records various statistics and graphs for contigs, including e.g. N75, N50 and N25 statistics, coverage distribution, contig size distributions.
• Read mapping in native Color Space
• Read mapping of Sanger, 454, Illumina Genome Analyzer, Helicos, and SOLiD sequencing data
• Read mapping of mixed datasets (e.g. 454 and Illumina Genome Analyser)
• Read mapping of genomes of any size
• Assembly of standard read data and support for assembly of paired end reads / mate pair reads of any sequencing technology
• Advanced graphical tools for detection of large scale mutations and rearrangements
  • Single reads - coverage and conflicts
  • Paired-ends reads - graphical overview
  • Paired-ends reads - insertions and deletions
  • Paired-ends reads - duplications and inversions
• Masking of read mapping based on annotations like e.g. exons
• Interactive and zoom-able viewing of genome assemblies, including sequencing reads, quality data, and reference sequences. Full integration of the viewers with the downstream analyses
• Advanced SNP detection, including choice of ploidity
• SNP reporting
• Advanced DIP detection, including choice of ploidity
• DIP reporting

Transcriptomics

The screen shot shows a table view of an expression sample generated from a sequence file of NGS mRNA reads. The table gives gene expression level values (read per kilo base of exon model: RPKM), along with statistics to the read counts, exons and transcripts. For each gene the assembly result may be opened, allowing examination of reads for that gene. (CLC Genomics Workbench - v.2.9 beta)
Figure 2 (click to enlarge):
A table view of an expression sample generated from an sequence file of NGS mRNA reads.
• Calculation of gene expression measures (RPKM) from mRNA sequence data and generation of gene expression profiles (RNA-Seq analysis)
• Full support for native Color Space
• RNA-seq outputs and can use unique and total gene/exon reads as well as median coverage as measures of expression.
• Small RNA analysis -Adapter trimming, Counting of tags, Annotation using miRBase and other resources, Visualization of miRNA variants and Expression analysis.
• Statistical tests for comparing expression levels of count-based expression measures.
  • Kal's test for differences of proportions in single sample to single sample comparisons.
  • Baggerley's test for differences of proportions in two groups with replicates comparisons.
• Discovery of novel transcripts/exons through mapping of mRNA reads to whole chromosomes or genomes, comparing matches with known exons
• Interactive views of assemblies and derived gene expression data
• Statistics on numbers of matching and unique gene, exon and exon-exon boundary spanning reads
• SNP and DIP detection can be performed directly on RNA-seq output contig tables
• Ability to work with Expression Arrays and RNA-seq results at the same time, enabling comparison of results
• Support for both microarray- and sequencing-based (RNA-Seq) expression data
• Visualization: Interactive heat map, table and scatter plot views
• Transformation and normalization tools
• Quality control tools including principal component analysis, MA- and boxplots
• Experimental design tools for two- or multiple group comparisons
• T-tests and ANOVA analysis with support for paired/repeated measures
• Multiple testing corrected p-values (Bonferroni and/or FDR)
• Clustering algorithms: hierarchical clustering, k-means and Partitioning Around Medoids (PAM) with support for various distance and linkage measures.
• Ability to import NetAffx annotation arrays and adding annotation to experiments
• Tools for Gene Set Enrichment Analysis (GSEA) and for Hyper-Geometric based tests for overrepresented annotation categories (e.g. 'GO'stats or specific protein pathways).
• Facility for annotating sequences from GFF or GTF files (as used by Ensembl and the UCSC Genome Browser), useful for annotating reference genomes before assembly

Epigenomics

• Chromatin immunoprecipitation sequencing (ChIP-seq) analysis
• Peak finding
• Peak refinement
• Graph and table of background distribution and false discovery rate
• Peak table and annotations

General NGS features

• Support for multiplex sequencing by file name
• Support for multiplex sequencing by sample-specific tag
• Integration with CLC bio’s High Performance Computing solutions, making assemblies very fast
• Quality reporting and statistics on raw data
• Filtering and trimming of reads
• Support for integration with CLC Bioinformatics Database
• Runs on Windows, Mac OS X, and Linux

CLC Genomics Workbench is fully integrated with CLC Assembly Cell, our command line solution for super fast assembly of Next Generation Sequencing data.

More features

CLC Genomics Workbench includes all features from CLC Main Workbench - all listed below:

RNA structure analysis

• Secondary structure prediction
• Graphical view and editing of secondary structure
• Tabular view of structures and energy contributions
• Symbolic representation in sequence view

DNA sequence analysis

• Editor for graphically and algorithmically advanced primer design
• In silico PCR
• Assembly of DNA sequence data
• Multiplexing - Process Tagged Sequences has an option to filter away groups with few sequences.
• Molecular cloning
• Gateway Cloning
• Automatic SNP annotation of sequences
• Local complexity region analyses
• Reverse translation from protein to gene, based on translation tables from a number of species
• Advanced restriction enzyme analysis and management
• Dot plot based analyses
• DNA statistics report including a number of characteristics of a given molecule
• NCBI sequence data search
• Access to web info from PubMed

Protein sequence analysis

• Integrated 3D molecule view
• Transmembrane helix prediction
• Antigenicity
• Secondary protein structure prediction
• PFAM domain search
• Web-based prediction of signal peptides and their cleavage sites (SignalP located on http://www.cbs.dtu.dk/services/SignalP/)
• Hydrophobicity analyses and graphs
• Protein charge analysis and graphs
• Reverse translation from protein to gene (a number of translation tables)
• Interactive translations of DNA and RNA to protein (both single sequences and alignments)
• Proteolytic cleavage detection
• Report of protein statistics (one or more proteins in each report)
• Comprehensive report including a range of protein analyses in one document

Pattern search

• Search for sequence matches
• Motif search for basic patterns
• Motif search using regular expressions
• Motif search with ProSite patterns
• Pattern discovery (unknown patterns)

Database searches

• Web-based sequence search using BLAST
• BLAST on local databases
• Build local BLAST databases
• GenBank Entrez searches
• UniProt searches (SwissProt/TrEMBL)
• PubMed lookup
• Web-based lookup in UniProt, NCBI, and Google
• SNP annotation using BLAST

Project and data management

• Full integration of data input, data management, calculation results, and data export
• Detailed history log
• All types of files can be saved in local projects, and launched from the program
• Import and export of data in a large number of file formats
• Option of working in several active workspaces at a time, enabling simultaneous work on multiple projects

Other bioinformatics features

• DNA, RNA and protein sequence editor displaying both linear and circular molecules
• Multiple alignment of DNA, RNA, and proteins
  
  • Two proprietary algorithms
  • ClustalW
  • Muscle
  • T-Coffee
  • MAFFT
  • Kalign
• Joining multiple alignments into one
• DNA, RNA, and protein alignment editor
• Interactive logo graphs along both DNA, RNA and Protein alignments
• Batch processing of analyses on multiple sequences in one work-step
• Advanced re-alignment and fix-point alignment option
• Manual annotation of sequences
• Dot plot based analyses
• Local complexity region analyses and complexity plots
• Gap fraction graphs
• G/C content analysis and graphs
• Advanced pairwise comparison
• Extract annotations