CLC Genomics Workbench our new solution for analyzing and visualizing Next Generation Sequencing data. CLC Genomics Workbench incorporates cutting-edge technology and algorithms, while also supporting and integrating with the rest of your typical NGS workflow.
CLC Genomics Workbench is very fast and allows you to do reference assembly of genomes of any size - the only limit is the amount of RAM on the machine running the software.
CLC Genomics Workbench is also able to support SNP detection, de novo assembly and a large number of downstream analysis.
Here are some key features of "CLC Genomics Workbench":
· De novo assembly of Sanger, 454, Illumina Genome Analyzer, Helicos, and SOLiD data.
· Reference assembly of Sanger, 454, Illumina Genome Analyzer, Helicos, and SOLiD sequencing data.
· Reference assembly of mixed datasets (e.g. 454 and Illumina Genome Analyser).
· Reference assembly 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.
· Support for multiplex sequencing by file name.
· Support for multiplex sequencing by sample-specific tag.
· Masking of reference assembly based on annotations like e.g. exons.
· Integration with CLC bio???s High Performance Computing solutions, making assemblies very fast.
· 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.
· Quality reporting and statistics on raw data.
· This wizard is used to handle parallel tagged sequence data. The use of tagged samples can dramatically increase sequencing throughput of next generation sequencers [1]. Analysis of this sample of mixed data is done by the Genomics Workbench.
· [1] Matthias Meyer, Udo Stenzel & Michael Hofreiter, "Parallel tagged sequencing on the 454 platform", Nature Protocols 3, - 267 - 278 (2008)
· This wizard is used to handle parallel tagged sequence data.
· Filtering and trimming of reads.
· Advanced SNP detection.
· SNP reporting.
· Support for integration with CLC Bioinformatics Database.
Requirements:
· 256 MB RAM required.
· 2 GB RAM recommended.
· 1024 x 768 display recommended.
· 3D viewing requires an OpenGL 3D graphics driver (included with almost all graphics cards).
· Assembly and analysis of genomes up to 10 mega-bases: 2 GB RAM required; 4 GB RAM recommended.
· Assembly and analysis of larger genomes: 2 GB RAM required; 8 GB RAM recommended.
· 64 bit computer and operating system recommended for more than 2 GB RAM.
Limitations:
· 30 days trial period.
What`s New in This Release: [ read full changelog ]
Bug fixes:
· De novo assembly produced empty results
· Paired distances for read mapping were not recorded correctly in history
· Read mapping in batch: the minimum and maximum paired distance fields were enabled even though the "Override" checkbox was unchecked
· Improved performance of packed view rendering
· Various minor bug-fixes
