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Limitations of next-generation genome sequence assembly


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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Figure 1: Summary of de novo genome assembly and new sequence analysis.

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We thank E. Karakoc and P. Sudmant for helpful discussions, T. Marques-Bonet and J.M. Kidd for providing the nonredundant gene table, and T. Brown for proofreading the manuscript. This work was partly supported by US National Institutes of Health grant HG002385 to E.E.E. E.E.E. receives funds as an Investigator of the Howard Hughes Medical Institute.

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Authors and Affiliations



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

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Correspondence to Evan E Eichler.

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Competing interests

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

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–2, Supplementary Table 2, Supplementary Note (PDF 402 kb)

Supplementary Table 1

Contamination found in reported human new sequence insertions from the genomes of two individuals. (XLS 406 kb)

Supplementary Table 3

Analysis of nonredundant autosomal genes in the YH genome assembly. (XLS 5110 kb)

Supplementary Table 4

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. (TXT 12294 kb)

Supplementary Table 5

Assigned positions of duplicated sequences (YH) to the NCBI build 36 assembly. (XLS 2229 kb)

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Alkan, C., Sajjadian, S. & Eichler, E. Limitations of next-generation genome sequence assembly. Nat Methods 8, 61–65 (2011).

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