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

Genome Res. 2010 Feb;20(2):265-72. doi: 10.1101/gr.097261.109. Epub 2009 Dec 17.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • African Continental Ancestry Group / genetics
  • Asian Continental Ancestry Group / genetics
  • Genome, Human*
  • Human Genome Project*
  • Humans
  • Oligonucleotide Array Sequence Analysis / economics
  • Oligonucleotide Array Sequence Analysis / methods
  • Sequence Alignment / economics
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / economics
  • Sequence Analysis, DNA / methods*