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Open Access Publications from the University of California

Assembly of Repeat Content Using Next Generation Sequencing Data

  • Author(s): labutti, Kurt
  • Kuo, Alan
  • Grigoriev, Igor
  • Copeland, Alex
  • et al.

Repetitive organisms pose a challenge for short read assembly, and typically only unique regions and repeat regions shorter than the read length, can be accurately assembled. Recently, we have been investigating the use of Pacific Biosciences reads for de novo fungal assembly. We will present an assessment of the quality and degree of repeat reconstruction possible in a fungal genome using long read technology. We will also compare differences in assembly of repeat content using short read and long read technology.

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