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The de novo assembler also combines datasets generated by different HTS instruments including those sold by Illumina, Roche, and Applied Biosystems. ![]() “If you use our algorithm, you can crunch a lot more data,” he says.ĬLC Bio’s de novo assembler works through an intuitive, user-friendly graphical as well as a command-line interface, according to Knudsen. The company then harnessed this built-in function to speed bioinformatics calculations. However, “our skilled computer programmers realized it was an ideal technology for bioinformatics, which also runs lots of parallel calculations,” says Knudsen. The MMX technology, added in 1996, was intended for handling complex graphics but never caught on. #CLC GENOMICS WORKBENCH NUMBER OF READS TOO LOW SOFTWARE#The software engineers at CLC Bio accomplished this by creating new data-compression algorithms to take advantage of computing power inherent in Intel microprocessors that generally lies dormant.Īll Intel microprocessors contain the MMX™ technology that runs many calculations in parallel. The company also adds that its assembler requires 48 gigabytes of RAM compared to others that need 300 gigabytes of RAM. CLC Bio says that its de novo assembler algorithm runs 50 times faster than existing products, and deciphers complete datasets in just a few hours. In March 2010, CLC Bio released a de novo assembler that constructs whole genomes of any size, including human and plant genomes, on a single workstation computer. He notes some key improvements to this version, including capabilities for parallel job executions on multiple computers through multiple job nodes, integration of third-party command-line tools and algorithms, support for file sharing and data management, and additional HTS analyses such as digital gene expression for RNA sequencing, SNP and DIP detection, and ChIP-seq analysis. Version 2.0 of the CLC Genomics Server includes a wider range of features for handling HTS data, says Knudsen. The company says that the server provides flexible options for executing centralized services, easy integration with other applications and services, powerful database communication and data integration, and a secure access control framework and central-action logging. CLC Bio describes the Genomics Server a bioinformatics solution built on a three-tier server architecture. “A key to our success is that our customers can mix data, and that will continue with new platforms,” he says.Įarly in 2010, the company released version 2.0 of the CLC Genomics Server, an enterprise platform for next-generation sequencing data analysis. This overlying strategy extends to software in development to handle the hundreds of thousands of reads generated by upcoming third-generation sequencers. Because different sequencing instruments offer different advantages, it makes sense to mix datasets into hybrid assemblies, Knudsen notes. Users of CLC Bio’s software are not locked into a single platform, but can use any or all HTS machines. “We had a head start in the market, making us a premiere solution provider.” When first launched, “no other companies were doing this,” says Knudsen. The CLC Genomics Workbench is a comprehensive package that analyzes and visualizes data from all major next-generation HTS platforms, such as SOLiD by Applied Biosystems, 454 GSflx by Roche, and Solexa by Illumina. “So there’s a critical demand for solutions that are really adept at handling and analyzing these huge amounts of data,” he says. In fact, the amount of genomic sequencing data increases 10-fold every 18 months. Whereas first-generation sequencing machines typically generate 0.1 megabases of data per run, second-generation instruments can spew out up to 40,000 megabases in a single run, explains Knudsen. The CLC Genomics Workbench, released in 2008, analyzes data from second-generation HTS instruments. In 2007, the company switched its focus to the analysis of next-generation sequencing data. Right: comparing expression across samples and clustering differentially expressed genes in a heat map Working with RNA-Seq data in CLC Genomics Workbench: Left: mapping of reads showing evidence of expression of three splice variants for this gene. ![]() Although designed for first-generation sequence data, he believes that the software makes a good teaching tool for students in molecular biology. #CLC GENOMICS WORKBENCH NUMBER OF READS TOO LOW HOW TO#When first launched, the software was “a powerful and intuitive way to show people how to do bioinformatics,” says Thomas Knudsen. In the first year, 100,000 downloads occurred, and by 2008, the number of downloads passed one million. #CLC GENOMICS WORKBENCH NUMBER OF READS TOO LOW FREE#The Sequence Viewer software remains free and can be downloaded from the company’s website. ![]()
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