We have overcome the challenge to analyze High-Throughput 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.
Details
Dominating the High-Throughput Sequencing data analysis challenge
We have overcome the challenge to analyze High-Throughput 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.
Some of the key Next Gen Sequencing applications of CLC Genomics Workbench are listed below
Genomics
Read mapping of Sanger, 454, Illumina Genome Analyzer and SOLiD sequencing data
De novo assembly of genomes of any size (only limited by RAM available)
Color space mapping
Advanced visualization, scrolling, and zooming tools
SNP detection using advanced quality filtering
Support for multiplexing with DNA barcoding
Transcriptomics
RNA-seq including support for paired data and transcript-level expression
Small RNA analysis
Expression profiling by tags
EST library construction
Advanced visualization, scrolling, and zooming tools
Gene expression analysis
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.
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.
Software Link: CLC Genomics Workbench
