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Metassembler: Merging and optimizing de novo genome assemblies

Alejandro Hernandez Wences, Michael C. Schatz
doi: https://doi.org/10.1101/016352
Alejandro Hernandez Wences
1Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
2Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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Michael C. Schatz
1Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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Abstract

Genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have complementary, if untapped, strengths and weaknesses. We present our metassembler algorithm that merges multiple assemblies of a genome into a single superior sequence. We apply it to the four genomes from the Assemblathon competitions and show it consistently and substantially improves the contiguity and quality of each assembly. We also develop guidelines for metassembly by systematically evaluating 120 permutations of merging the top 5 assemblies of the first Assemblathon competition. The software is open-source at http://metassembler.sourceforge.net.

  • Abbreviations

    CEGMA -
    Core Eukaryotic Genes Mapping Approach
    CE-statistic -
    Compression/Expansion statistic
    Comp Ref Bases -
    Compressed Reference Bases
    Ctg NG50 -
    Contig N50 size relative to the estimated/reference genome size
    Ctg GC-NG50 -
    Contig GAGE Corrected N50, relative to the reference genome size Ctg RC-NG50 - Contig REAPR Corrected N50, relative to the estimated genome size Dup Ref Bases - Duplicated Reference Bases
    GAGE -
    Genome Assembly Gold Standard Evaluation
    GAM-NGS -
    Genomic Assemblies Merger for Next Generation Sequencing
    ICA -
    Independent Component Analysis
    PCA -
    Principal Components Analysis
    REAPR -
    Recognising Errors in Assemblies using Paired Reads
    Scf NG50 -
    Scaffold N50 size relative to the estimated/reference genome size
    Scf GC-NG50 -
    Scaffold GAGE Corrected N50, relative to the reference genome size
    Scf RC-NG50 -
    Scaffold REAPR Corrected N50, relative to the estimated genome size
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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    Posted March 10, 2015.
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    Metassembler: Merging and optimizing de novo genome assemblies
    Alejandro Hernandez Wences, Michael C. Schatz
    bioRxiv 016352; doi: https://doi.org/10.1101/016352
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    Metassembler: Merging and optimizing de novo genome assemblies
    Alejandro Hernandez Wences, Michael C. Schatz
    bioRxiv 016352; doi: https://doi.org/10.1101/016352

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