FSG: Fast String Graph Construction for De Novo Assembly

@article{Bonizzoni2017FSGFS,
  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},
  year={2017},
  volume={24 10},
  pages={
          953-968
        }
}
  • 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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    References

    SHOWING 1-10 OF 33 REFERENCES
    Efficient construction of an assembly string graph using the FM-index
    • 231
    • Highly Influential
    • PDF
    Readjoiner: a fast and memory efficient string graph-based sequence assembler
    • 48
    • PDF
    LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly
    • 16
    The fragment assembly string graph
    • E. Myers
    • Mathematics, Medicine
    • ECCB/JBI
    • 2005
    • 383
    • Highly Influential
    • PDF
    Efficient de novo assembly of large genomes using compressed data structures.
    • 688
    • Highly Influential
    • PDF
    Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly
    • Heng Li
    • Biology, Medicine
    • Bioinform.
    • 2012
    • 270
    • PDF
    On the representation of de Bruijn graphs
    • 79
    • PDF
    Variable-Order de Bruijn Graphs
    • 45
    • PDF
    String graph construction using incremental hashing
    • 15
    • PDF
    Space-efficient and exact de Bruijn graph representation based on a Bloom filter
    • R. Chikhi, G. Rizk
    • Computer Science, Medicine
    • Algorithms for Molecular Biology
    • 2012
    • 265
    • PDF