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The phusion assembler.

James C Mullikin1, Zemin Ning

  • 1Informatics Department, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. jcm@sanger.ac.uk

Genome Research
|January 17, 2003
PubMed
Summary
This summary is machine-generated.

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The Phusion assembler successfully generated a high-quality draft assembly of the mouse genome using whole-genome shotgun sequencing data. This advanced assembly method also proved effective for the Caenorhabditis briggsae genome.

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • The Mouse Genome Sequencing Consortium generated whole-genome shotgun (WGS) data for the mouse genome.
  • Large, repeat-rich genomes present challenges for accurate assembly.
  • Paired-end sequencing data with varying insert sizes is crucial for complex genome assembly.

Purpose of the Study:

  • To present the high-quality draft assembly of the mouse genome using the Phusion assembler.
  • To demonstrate the effectiveness of Phusion for assembling large and repeat-rich genomes.
  • To report on the WGS assembly of Caenorhabditis briggsae using Phusion.

Main Methods:

  • Utilized the Phusion assembler for whole-genome shotgun (WGS) data.
  • Employed paired-end sequencing reads with insert sizes ranging from 2-200 kbp.

Related Experiment Videos

  • Implemented a preassembly stage to cluster reads for parallelized assembly.

    • Main Results:

    • Achieved a high-quality draft assembly of the mouse genome (2.6 gigabases) with ~7.5x coverage.
    • 90% of the mouse genome assembly is contained within 479 scaffolds.
    • Successfully assembled the Caenorhabditis briggsae genome with ~11x coverage.

    Conclusions:

    • Phusion is an effective assembler for large, repeat-rich genomes like the mouse.
    • The preassembly clustering approach facilitates parallelization and efficient genome assembly.
    • Phusion provides accurate results for complex genomic datasets.