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De novo assembly of human genomes with massively parallel short read sequencing

    • 1 Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China;
    • 2 Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark
    • 3 These authors contributed equally to this work.
    • 4 Corresponding author. E-mail [email protected]; fax 86-755-25274247.
Published December 17, 2009. Vol 20 Issue 2, pp. 265-272. https://doi.org/10.1101/gr.097261.109
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cover of Genome Research Vol 36 Issue 4
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April 2026, Vol. 36, No. 4
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Abstract

Next-generation massively parallel DNA sequencing technologies provide ultrahigh throughput at a substantially lower unit data cost; however, the data are very short read length sequences, making de novo assembly extremely challenging. Here, we describe a novel method for de novo assembly of large genomes from short read sequences. We successfully assembled both the Asian and African human genome sequences, achieving an N50 contig size of 7.4 and 5.9 kilobases (kb) and scaffold of 446.3 and 61.9 kb, respectively. The development of this de novo short read assembly method creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost-effective way.

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