Marta Matvienko, Sr. Field Application Specialist. PAG XXII. January 14 ... Cross-platform desktop application with a graphical user-interface ... Create Track List.
Sample & Assay Technologies
Overview of tools and workflows in CLC Genomics Workbench and Microbial Genome Finishing Module
PAG XXII January 14, 2014
Marta Matvienko, Sr. Field Application Specialist
Sample & Assay Technologies
Advanced bioinformatics and User-friendliness
Overview of tools and workflows in CLC Genomics Workbench and Microbial Genome Finishing Module, January 14, 2014, PAG XXII
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Sample & Assay Technologies
CLC bio Products
Products for Genomics 1. Stand-alone Applications Genomics Workbench Main Workbench Assembly Cell 2. Enterprise Solutions Genomics Server 3. Clients to the server Genomics Workbench Command Line Tools
4. Plugins Released and ready-to-use plugins Custom Plugins from our Consulting Free SDK for Do-it-yourself plugins
Overview of tools and workflows in CLC Genomics Workbench and Microbial Genome Finishing Module, January 14, 2014, PAG XXII
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Products for NGS data analysis
Sample & Assay Technologies
Enterprise Solutions
Stand-alone Applications
Genomics Workbench
CLC Assembly Cell
Overview of tools and workflows in CLC Genomics Workbench and Microbial Genome Finishing Module, January 14, 2014, PAG XXII
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Sample & Assay Technologies
Products in Detail
Microbial Genome Finishing Module
Genomics Workbench
Cross-platform desktop application with a graphical user-interface
Overview of tools and workflows in CLC Genomics Workbench and Microbial Genome Finishing Module, January 14, 2014, PAG XXII
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Sample & Assay Technologies
Supported Applications and Tools
Overview of tools and workflows in CLC Genomics Workbench and Microbial Genome Finishing Module, January 14, 2014, PAG XXII
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Sample & Assay Technologies
New Features and Improvements in GWB v7
Complete redesign of the graphical user interface New concept for Side Panels and Views • • • •
Support for multiple screens: views can be moved to a different screen by dragging the tab of the view Side Panels now consist of palettes that can be organized in group and the order can be customized Palettes can be detached and placed anywhere on the screen Navigation Area and Toolbox can be minimized to allow more space for displaying data
Zoom tools redesign • • •
The zoom tools have been re-organized and placed closer to the data Detailed zoom is a new feature that allows zooming in and out in very small increments Zoom to selection button now available for track views
Overview of tools and workflows in CLC Genomics Workbench and Microbial Genome Finishing Module, January 14, 2014, PAG XXII
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Sample & Assay Technologies
New Features and Improvements in GWB v7 RNA-Seq on tracks
• gene level track • transcript level track
Overview of tools and workflows in CLC Genomics Workbench and Microbial Genome Finishing Module, January 14, 2014, PAG XXII
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Sample & Assay Technologies
New Features and Improvements in GWB v7 RNA-Seq experiments can be used for browsing the track list with read mappings and annotations.
Overview of tools and workflows in CLC Genomics Workbench and Microbial Genome Finishing Module, January 14, 2014, PAG XXII
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Sample & Assay Technologies
New Features and Improvements in GWB v7 RNA-Seq continued…
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Variant tracks can be annotated with expression values from expression tracks
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New statistical test based on EdgeR, for comparisons of pairs of groups, performs TMM normalization (Robinson and Smyth)
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The old RNA-Seq Analysis tool is available as a plugin
Overview of tools and workflows in CLC Genomics Workbench and Microbial Genome Finishing Module, January 14, 2014, PAG XXII
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Sample & Assay Technologies
New Features and Improvements in GWB v7 Phylogenetic Analysis
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Greatly enhanced viewer for visualizing and working with phylogenetic trees
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Supports importing, editing and visualization of metadata associated with nodes in phylogenetic trees
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Tool to reconstruct phylogenetic trees based on k-mers - useful for whole genome phylogenetic reconstruction where the genomes are closely related
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Tool performing a statistic evaluation of different substitution models to be used with maximum likelihood tree construction
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And number of other additions/improvements
Overview of tools and workflows in CLC Genomics Workbench and Microbial Genome Finishing Module, January 14, 2014, PAG XXII
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Sample & Assay Technologies
New Features and Improvements in GWB v7 Phylogenetic Analysis
Overview of tools and workflows in CLC Genomics Workbench and Microbial Genome Finishing Module, January 14, 2014, PAG XXII
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Sample & Assay Technologies
New Features and Improvements in GWB v7 New in Workflows
1. Bulk configuration of elements enables to set the same reference data for multiple elements at once
2. Workflows can be added inside a workflow. The inner workflow is "unfolded" into the single elements 3. New tools that are now workflowenabled: • • • •
Create Track List Annotate with Flanking Sequences Convert from Tracks All tools in Statistical Tests
Overview of tools and workflows in CLC Genomics Workbench and Microbial Genome Finishing Module, January 14, 2014, PAG XXII
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Sample & Assay Technologies
CLC MICROBIAL GENOME FINISHING MODULE To produce high quality assemblies in sequencing projects
Finishing Module Toolbox in Jan 2013
Finishing Module Toolbox in Jan 2014
Overview of tools and workflows in CLC Genomics Workbench and Microbial Genome Finishing Module, January 14, 2014, PAG XXII
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Sample & Assay Technologies
CLC MICROBIAL GENOME FINISHING MODULE
Overview of tools and workflows in CLC Genomics Workbench and Microbial Genome Finishing Module, January 14, 2014, PAG XXII
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Sample & Assay Technologies
CLC MICROBIAL GENOME FINISHING MODULE Join Contigs Tool (beta)
Overview of tools and workflows in CLC Genomics Workbench and Microbial Genome Finishing Module, January 14, 2014, PAG XXII
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Sample & Assay Technologies
New Features and Improvements
GWB 7 – entire list of new features and improvements http://www.clcbio.com/products/latest-improvements/ MGFM http://www.clcbio.com/products/clc-microbial-genome-finishing-module/
clcbio.com Products 2 week trials
CLC bio websites too: clcagro.com clcbio.tv clcsupport.com
Overview of tools and workflows in CLC Genomics Workbench and Microbial Genome Finishing Module, January 14, 2014, PAG XXII
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Sample & Assay Technologies
Thank you! Questions?
Overview of tools and workflows in CLC Genomics Workbench and Microbial Genome Finishing Module, January 14, 2014, PAG XXII
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