FSG: Fast String Graph Construction for De Novo Assembly

  title={FSG: Fast String Graph Construction for De Novo Assembly},
  author={P. Bonizzoni and G. D. Vedova and Yuri Pirola and M. Previtali and R. Rizzi},
  journal={Journal of computational biology : a journal of computational molecular cell biology},
  volume={24 10},
  • P. Bonizzoni, G. D. Vedova, +2 authors R. Rizzi
  • Published 2017
  • Mathematics, Medicine, Computer Science, Biology
  • Journal of computational biology : a journal of computational molecular cell biology
  • The string graph for a collection of next-generation reads is a lossless data representation that is fundamental for de novo assemblers based on the overlap-layout-consensus paradigm. In this article, we explore a novel approach to compute the string graph, based on the FM-index and Burrows and Wheeler Transform. We describe a simple algorithm that uses only the FM-index representation of the collection of reads to construct the string graph, without accessing the input reads. Our algorithm has… CONTINUE READING
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