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Dominating the Next Generation Sequencing data analysis challenge
We have overcome the challenge to analyze Next Generation Sequencing data faster than it is produced by implementing a SIMD-accelerated assembly algorithm in our Next Generation Sequencing solution, CLC Genomics Workbench - a cross-platform desktop application with a graphical user-interface.
CLC Genomics Workbench, for analyzing and visualizing Next Generation Sequencing data, incorporates cutting-edge technology and algorithms, while also supporting and integrating with the rest of your typical NGS workflow.
Get a free trial of CLC Genomics Workbench for two weeks!
Some of the key Next Gen Sequencing applications of CLC Genomics Workbench are listed below
Genomics
- Whole genome re-sequencing and targeted re-sequencing of genomes of any size and type – from bacteria and vira to humans
- De novo assembly of an unlimited number of reads, for genomes up to human size
- SNP/DIP detection and identification of genomic rearrangements
- Visualization and interactive graphical manipulation of results
Transcriptomics
- Digital Gene Expression based on RNA-Seq, including a wide range of downstream gene expression analyses
- Discovery of novel transcripts/exons
- Ability to work with Expression Arrays and RNA-seq results at the same time, enabling comparison of results
- Interactive views of assemblies and derived gene expression data
- Small RNA-seq
- Tag Profiling, including SAGE screen analyses
Epigenomics
- Chromatin immunoprecipitation sequencing (ChIP-seq) analysis
- Peak finding and peak refinement
- Graph and table of background distribution and false discovery rate
- Peak table and annotations
Cross-platform
CLC Genomics Workbench is available for Windows, Mac OS X, and Linux platforms, and includes all features of CLC Main Workbench for carrying out a wide range of downstream analyses.Benchmarking
In benchmark tests we have assembled half a million 454 reads against the full E. coli reference genome in around 2 minutes on a two-core laptop with 2 gigabyte RAM. This speed-up, based on integrated SIMD high-performance computing technology, increases even more when using a computer with more CPU-cores and RAM.
| A few benchmarks - E. Coli | Time (minutes) |
| 454: Read mapping and visualization of 439,000 reads to E. Coli (5 mega bases) on a 1,500 USD 2GB dual core, 2.13 GHz, 32 bit laptop computer | 2 |
| Illumina Genome Analyzer: Read mapping and visualization of 2 x 2.7 = 5.4 million paired end reads (1 lane) to E. Coli (5 Mega bases) on a 32GB, 8 core, 2.5 GHz, 64 bit desktop computer | 3 |
| A few benchmarks - Human | Time (hours) |
| Illumina Genome Analyzer: Read mapping and visualization of 2 x 43 million = 86 million paired end reads to Human (3 Giga bases) on a 32GB, 8 core, 2.5 GHz, 64 bit desktop computer (ungapped alignment) | 4 |
| Illumina Genome Analyzer: Read mapping and visualization of 2 x 43 million = 86 million paired end reads to Human (3 Giga bases) on a 32GB, 8 core, 2.5 GHz, 64 bit desktop computer (gapped alignment) | 7 |
If you need more calculation power, then integrate CLC Genomics Workbench with CLC Assembly Cell and/or CLC Science Server.
454, SOLiD, Illumina Genome Analyzer - no problem!
We support all the major Next Generation Sequencing platforms, such as SOLiD, 454, Illumina Genome Analyzer and of course also Sanger. We are working closely together with all the instrument vendors to ensure full integration in the ongoing development.
Product sheet & User Manual |
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CLC Genomics Workbench (Product Sheet) 4 pages - 1 MB |
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CLC Genomics Workbench (User manual) 641 pages - 17.5 MB |
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