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Test driving genome assemblers

Nature Biotechnology volume 30, pages 330–331 (2012)Cite this article

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Two head-to-head comparisons of genome assembly methods highlight the best performers and outstanding problems.

Next-generation sequencing and new software for assembling reads are intended to provide economical, efficient ways of generating genome sequences de novo—but just how good are the resulting assemblies? Two recent papers1,2 in Genome Research describe the results of independent projects, the genome assembly gold-standard evaluation (GAGE)1 and the Assemblathon2, which evaluated a total of eight assemblers1 and assemblies submitted by 17 groups2. Both studies find that although genomes can be readily assembled at high coverage and accuracy, there is room for improvement, and that the assembly of large mammalian or plant genomes based on next-generation sequencing data alone remains challenging.

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Figure 1: Generating a genome sequence by next-generation sequencing and de novo assembly.

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Affiliations

  1. Wei Fan and Ruiqiang Li are in the Peking-Tsinghua Center for Life Sciences, Biodynamic Optical Imaging Center and School of Life Sciences, Peking University, Beijing, China.

    Wei Fan & Ruiqiang Li

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  1. Wei Fan
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  2. Ruiqiang Li
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Correspondence to Ruiqiang Li.

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The authors declare no competing financial interests.

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Fan, W., Li, R. Test driving genome assemblers. Nat Biotechnol 30, 330–331 (2012). https://doi.org/10.1038/nbt.2172

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