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sequencer: Simulate Shotgun Sequencing

Bernhard Haubold

Shotgun sequencing is a method for determining the nucleotide sequence of DNA molecules that are longer than a few kilo bases. Millions of exact copies of one such molecule are broken into overlapping short fragments and sequenced. The resulting reads are assembled into the sought template sequence using a computer program. To test such assembly programs, it is often useful to simulate reads and this is the purpose of sequencer. It takes as input a template DNA sequence and outputs random reads until the number of sequenced nucleotides divided by the length of the template molecule has reached a threshold known as the coverage.

  1. Source code
  2. Example data

Bernhard Haubold 2009-12-02