CLC Genomics Workbench

Genomics

• Genome browser
  
• Tracks
  
• 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
  
• 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
  
• Probabilistic Variant Detection, including choice of ploidity
  
• Quality-based Variant Detection
  
• Structural_Variation_Plugin_User_Manual like insertions, deletions, and interchromosomal variations

Transcriptomics

• 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
  
• 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.

Additionally, CLC Genomics Workbench includes all features of CLC Main Workbench as 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
  
• Multi-Site Gateway Cloning
  
• 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

Pattern search

• 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

Project and data management

• Full integration of data input, data management, calculation results, and data export
  
• Workflows can be built in the workbench to combine various tools from the toolbox into one analysis
  
• 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
  
• 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
  
• Gap fraction graphs
  
• G/C content analysis and graphs
  
• Advanced pairwise comparison
  
• Extract annotations

CLC Main Workbench

Expression analysis including digital gene expression

• Support for both microarray- and sequencing-based (post-mapping RNA-Seq) expression data
  
• Visualization: Interactive heat map
  
• Visualization: Scatter plots
  
• Transformation and normalization tools
  
• Quality control tools including principal component analysis, MA- and box plots
  
• 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)
  

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
  
• Multi-Site Gateway Cloning
• 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
  

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
  

Pattern search

• 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
  

Project and data management

• Full integration of data input, data management, calculation results, and data export
  
• Workflows can be built in the workbench to combine various tools from the toolbox into one analysis
  
• 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 (link to file format page in Support area)
  
• 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
  
• 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
  
• Local complexity region analyses and complexity plots
  
• Gap fraction graphs
  
• G/C content analysis and graphs
  
• Advanced pairwise comparison
  
• Extract annotations

CLC Sequence Viewer

Bioinformatics features

• Multiple alignment of DNA, RNA, and proteins
  Two proprietary algorithms
  ClustalW
  Muscle
  
• Consensus sequence determination and management
  
• Conservation score along alignments
  
• Open reading frame determination
  
• Easy access to web-based protein and nucleotide search in GenBank, including download facilities and full graphical overview of sequence annotations of your choice
  
• Translation from DNA to protein (all genetic translation tables)
  
• Reports with residue composition, molecular weight and iso electric point (for proteins)
  
• Neighbor-joining and UPGMA phylogenies
  
• Restriction site analysis and viewing
  
• Create reverse complement
  
• Shuffle sequence
  
• Option of viewing and graphical manipulation of bioinformatics analyses made in commercial workbenches from CLC bio
  

Other features

• Full integration of data input, data management, calculations results, and data export. This eliminates time spent on manual data transfers between different programs and databases
  
• All types of files can be saved in local projects and launched from the program
  
• Detailed history log
  
• User-friendly graphical tools used in order to find and work with relevant regions of DNA, RNA and protein sequences
  
• Text-based sequence view
  
• Easy printing of reports and graphics
  
• Export of user-defined figures to various graphics file formats
• Import and export of data in a large number of file formats
  
• Option of working with different files and in different file projects at the same time
  
• Option of working in several active workspaces at a time, enabling simultaneous work on multiple projects