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.

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
   PLoS ONE 6(9): e24711.
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
   Human Mutation 32(2):E1999–E2017, February 2011.
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
   Animal Genetics. Volume 41, Issue 2, pages 159–168, April 2010.
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
   Insect Biochemistry and Molecular Biology (2010) 40(1):79-90.
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
   BMC Genomics 2009, 10:264.
6. SLIPPER: An Iterative Mapping Pipeline for Short DNA Sequences
   Lee Edsall, Bing Ren & Terry Gaasterland
   Poster, ISMB 2008