TimeLogic,
Applications

Next-Gen Sequencing

With over 600 next-generation sequencing instruments now deployed across both large core facilities and individual research labs, enormous amounts of sequence data need to be analyzed. Unquestionably, the continual development of ultra high-throughput DNA sequencing technology is transforming genomics, but new bottlenecks in sequence alignment and downstream annotation have been created in the process. Our powerful field programmable gate array (FPGA) technology, SeqCruncher™, enables the comparison of millions of sequences against thousands of genomic databases in a convenient low-form factor solution.

TimeLogic customers are implementing our applications for various phases of their pipelines, often for high-sensitivity remapping of short-read sequences to improve their mapping percentage, and for direct analysis of 454 data and assembled contigs.

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Related Scientific Citations

Below is a short list of some recent DeCypher citations for Next Generation Sequencing. For the complete list, please vist our citations page here.

  1. First Transcriptome of the Testis-Vas Deferens-Male Accessory Gland and Proteome of the Spermatophore from Dermacentor variabilis (Acari: Ixodidae)
    Daniel E. Sonenshine, Brooke W. Bissinger, Noble Egekwu, Kevin V. Donohue, Sayed M. Khalil, R. Michael Roe
  2. Massive Parallel DNA Pyrosequencing Analysis Of The Tumor Suppressor BRG1/SMARCA4 In Lung Primary Tumors
    Salvador Rodriguez-Nieto, Andres Cañanda, Eva Pros, Ana Pinto, Juan Torres-Lanzas, Fernando Lopez-Rios, Lydia Sanchez-Verde, David Pisano, Montse Sanchez-Cespedes
  3. MicroRNA identity and abundance in porcine skeletal muscles determined by deep sequencing.
    M. Nielsen, J. H. Hansen, J. Hedegaard, R. O. Nielsen, F. Panitz, C. Bendixen, B. Thomsen
  4. Neuropeptide signaling sequences identified by pyrosequencing of the American dog tick synganglion transcriptome during blood feeding and reproduction
    Kevin V. Donohue, Sayed M.S. Khalil, E. Ross, Christina M. Grozinger, Daniel E. Sonenshine and R. Michael Roe
  5. Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing.
    Shrinivasrao P Mane, Clive Evans, Kristal L Cooper, Oswald R Crasta, Otto Folkerts, Stephen K Hutchison, Timothy T Harkins, Danielle Thierry-Mieg, Jean Thierry-Mieg and Roderick V Jensen
  6. SLIPPER: An Iterative Mapping Pipeline for Short DNA Sequences
    Lee Edsall, Bing Ren & Terry Gaasterland