Constructing String Graphs in External Memory

@inproceedings{Bonizzoni2014ConstructingSG,
  title={Constructing String Graphs in External Memory},
  author={P. Bonizzoni and G. D. Vedova and Yuri Pirola and M. Previtali and R. Rizzi},
  booktitle={WABI},
  year={2014}
}
  • P. Bonizzoni, G. D. Vedova, +2 authors R. Rizzi
  • Published in WABI 2014
  • Computer Science, Biology
  • In this paper we present an efficient external memory algorithm to compute the string graph from a collection of reads, which is a fundamental data representation used for sequence assembly. 
    12 Citations
    LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly
    • 16
    An External-Memory Algorithm for String Graph Construction
    • 13
    • PDF
    A New Lightweight Algorithm to compute the BWT and the LCP array of a Set of Strings
    • 3
    • PDF
    FSG: Fast String Graph Construction for De Novo Assembly
    • 16
    • PDF
    External memory BWT and LCP computation for sequence collections with applications
    • 4
    A representation of a compressed de Bruijn graph for pan-genome analysis that enables search
    • 16
    External memory BWT and LCP computation for sequence collections with applications
    • 14
    • PDF

    References

    SHOWING 1-10 OF 15 REFERENCES
    The fragment assembly string graph
    • E. Myers
    • Mathematics, Medicine
    • ECCB/JBI
    • 2005
    • 395
    • Highly Influential
    • PDF
    Lightweight Data Indexing and Compression in External Memory
    • 87
    • PDF
    Efficient construction of an assembly string graph using the FM-index
    • 238
    • Highly Influential
    • PDF
    Lightweight algorithms for constructing and inverting the BWT of string collections
    • 78
    • Highly Influential
    Suffix Arrays for Multiple Strings: A Method for On-Line Multiple String Searches
    • F. Shi
    • Computer Science
    • ASIAN
    • 1996
    • 27
    Lightweight LCP Construction for Next-Generation Sequencing Datasets
    • 30
    • PDF
    Efficient de novo assembly of large genomes using compressed data structures.
    • 702
    • PDF
    IDBA - A Practical Iterative de Bruijn Graph De Novo Assembler
    • 243
    • PDF
    Comparing DNA Sequence Collections by Direct Comparison of Compressed Text Indexes
    • 22
    • Highly Influential
    • PDF
    ABySS: a parallel assembler for short read sequence data.
    • 3,048
    • PDF