De Novo Sequencing

The initial generation of the primary genetic sequence of a particular organism is called de novo sequencing. A detailed genetic analysis of any organism is possible only after de novo sequencing has been performed.

De novo sequencing is typically accomplished by assembling individual sequence reads into longer contiguous sequences (contigs) or correctly ordered contigs (scaffolds) in the absence of a reference sequence.

Methods for De Novo Sequencing

Historically, de novo sequencing was carried out using capillary electrophoresis (CE) sequencers. With its long read lengths and high accuracy, CE-based sequencing made overlap consensus assembly the gold-standard technology for de novo projects. However, more recently, the high-throughput capabilities of massively parallel sequencing and the development of short-read assemblers have significantly reduced the time and cost associated with sequencing an entire genome.

De Novo Sequencing With the 5500xl Genetic Analyzer
  • Excellent coverage—throughput of as much as 30 Gb per day or more gives you the coverage you need for genome assembly
  • Greater confidence—Exact Call Chemistry provides accuracy up to 99.99%, delivering more confident assembly with less coverage
  • Flexibility in the assembler you choose—option of base space or color space output allows you to use the assembler of your choice

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De novo Sequencing Sample Prep for Next Generation Sequencing


De novo sequencing yields a primary genetic sequence of a particular organism where it may not previously be available.  It is necessary to first perform de novo sequencing in order to further analyze the genetic information of an organism in more detail.  As the sequencing of an organism can be a lengthy and costly endeavor through traditional sequencing methods, the capabilities of next generation sequencing technologies empower the progress of de novo sequencing efforts.

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De Novo Sequencing With the 3500 Genetic Analyzer
  • Generate long scaffolds—long reads and accuracy enable generation of long scaffolds using overlapping consensus assembly
  • Accurate and reliable detection—higher optical sensitivity and advanced polymers help you obtain higher-quality data at a lower cost
  • Automated approach—more than 24 hours of unattended operation; multiple automation features reduce human errors
  • Reproducibility—optimized polymers increase productivity without affecting the results

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For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use.

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