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Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

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Published on: August 20, 2021

Readjoiner: a fast and memory efficient string graph-based sequence assembler.

Giorgio Gonnella1, Stefan Kurtz

  • 1Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany.

BMC Bioinformatics
|May 8, 2012
PubMed
Summary
This summary is machine-generated.

New methods for constructing assembly string graphs improve de novo sequence assembly. Readjoiner software efficiently builds these graphs, offering faster and more space-efficient de novo sequence assembly compared to existing tools.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Next-generation sequencing technologies present challenges for de novo sequence assemblers.
  • Current assemblers often rely on de Bruijn graphs, but assembly string graphs offer an alternative framework.
  • Assembly string graphs require efficient algorithms for computing suffix-prefix matches between sequencing reads.

Purpose of the Study:

  • To develop efficient methods for constructing assembly string graphs.
  • To present algorithms for computing suffix-prefix matches among sequencing reads.
  • To implement these algorithms in a software package for de novo sequence assembly.

Main Methods:

  • Utilized suffix sorting and scanning methods to compute suffix-prefix matches.
  • Developed algorithms for early recognition and elimination of transitive edges in the string graph.
  • Focused on constructing string graphs containing only irreducible edges.

Main Results:

  • Efficient methods for string graph construction from sequencing reads were developed.
  • Algorithms effectively compute suffix-prefix matches and construct the graph.
  • The resulting string graphs are efficiently constructed with only essential edges.

Conclusions:

  • The Readjoiner software package implements novel suffix-prefix match determination and string graph construction algorithms.
  • Readjoiner demonstrates superior speed and space efficiency compared to existing string graph-based assemblers.
  • Readjoiner is available for use in de novo sequence assembly projects.