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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
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From sequence mapping to genome assemblies.

Thomas D Otto1

  • 1Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK, tdo@sanger.ac.uk.

Methods in Molecular Biology (Clifton, N.J.)
|November 13, 2014
PubMed
Summary
This summary is machine-generated.

Next-generation sequencing enables advanced research, but data processing requires careful mapping or de novo assembly. This chapter details de novo assembly improvements for high-quality draft genomes.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Next-generation sequencing technologies have expanded research capabilities.
  • Sequence data analysis typically involves mapping to a reference or de novo assembly.

Purpose of the Study:

  • To discuss limitations of sequence mapping and introduce de novo assembly.
  • To describe methods for improving de novo assembly quality.

Main Methods:

  • Local sequence assembly to overcome mapping limitations.
  • De novo assembly including scaffolding, contig ordering, and gap closure.
  • Error evaluation, gene annotation transfer, and ab initio gene annotation.

Main Results:

  • High-quality draft assemblies are achievable through advanced de novo assembly techniques.
  • Improved assemblies facilitate more informative downstream analyses.

Conclusions:

  • De novo assembly is crucial for generating high-quality genome drafts.
  • Optimized assembly procedures enhance the utility of sequencing data for diverse research applications.