Limitations of next-generation genome sequence assembly

Journal name:
Nature Methods
Year published:
Published online


High-throughput sequencing technologies promise to transform the fields of genetics and comparative biology by delivering tens of thousands of genomes in the near future. Although it is feasible to construct de novo genome assemblies in a few months, there has been relatively little attention to what is lost by sole application of short sequence reads. We compared the recent de novo assemblies using the short oligonucleotide analysis package (SOAP), generated from the genomes of a Han Chinese individual and a Yoruban individual, to experimentally validated genomic features. We found that de novo assemblies were 16.2% shorter than the reference genome and that 420.2 megabase pairs of common repeats and 99.1% of validated duplicated sequences were missing from the genome. Consequently, over 2,377 coding exons were completely missing. We conclude that high-quality sequencing approaches must be considered in conjunction with high-throughput sequencing for comparative genomics analyses and studies of genome evolution.


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Author information


  1. Department of Genome Sciences, University of Washington School of Medicine and Howard Hughes Medical Institute, Seattle, Washington, USA.

    • Can Alkan,
    • Saba Sajjadian &
    • Evan E Eichler


C.A. and E.E.E. conceived the study and wrote the manuscript. C.A. and S.S. analyzed the data.

Competing financial interests

E.E.E. is a scientific advisory board member of Pacific Biosciences.

Corresponding author

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Supplementary information

PDF files

  1. Supplementary Text and Figures (404 KB)

    Supplementary Figures 1–2, Supplementary Table 2, Supplementary Note

Excel files

  1. Supplementary Table 1 (408 KB)

    Contamination found in reported human new sequence insertions from the genomes of two individuals.

  2. Supplementary Table 3 (5 MB)

    Analysis of nonredundant autosomal genes in the YH genome assembly.

  3. Supplementary Table 5 (2 MB)

    Assigned positions of duplicated sequences (YH) to the NCBI build 36 assembly.

Text files

  1. Supplementary Table 4 (12 MB)

    Analysis of nonredundant autosomal coding exons in the YH genome. NOTE: This is a tab-delimited text file with 171,751 rows of data. Confirm that all data will load into your application before proceeding.

Additional data