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
  • Medicine, Computer Science, Mathematics, 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
    SOF: An Efficient String Graph Construction Algorithm
    • 1
    • Highly Influenced
    Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era
    • 2
    • PDF
    GPU-Accelerated Large-Scale Genome Assembly
    • 3
    Efficient String Graph Construction Algorithm
    Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly


    Publications referenced by this paper.
    Efficient de novo assembly of large genomes using compressed data structures.
    • 682
    • Highly Influential
    • PDF
    Efficient construction of an assembly string graph using the FM-index
    • 229
    • Highly Influential
    • PDF
    The fragment assembly string graph
    • 381
    • Highly Influential
    • PDF
    Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly
    • 264
    • PDF
    ABySS: a parallel assembler for short read sequence data.
    • 2,969
    • PDF
    Readjoiner: a fast and memory efficient string graph-based sequence assembler
    • 48
    • PDF
    Space-efficient and exact de Bruijn graph representation based on a Bloom filter
    • 261
    • PDF
    On the representation of de Bruijn graphs
    • 76
    • PDF
    GAGE: A critical evaluation of genome assemblies and assembly algorithms.
    • 660
    • PDF