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PMID: 20019144 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

Genome research ·Vol. 20 ·No. 2 ·2010-02-00 ·Pages 265-72

Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J

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.

MeSH Terms
Asians/genetics Blacks/genetics Genome, Human Human Genome Project Humans Oligonucleotide Array Sequence Analysis/economics,methods Sequence Alignment/economics,methods Sequence Analysis, DNA/economics,methods
Authors & Affiliations
14 authors, click to expand affiliations / ORCID
Li Ruiqiang
Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China.
Zhu Hongmei
Ruan Jue
Qian Wubin
Fang Xiaodong
Shi Zhongbin
Li Yingrui
Li Shengting
Shan Gao
Kristiansen Karsten
Li Songgang
Yang Huanming
Wang Jian
Wang Jun
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1549-5469
DOI
10.1101/gr.097261.109
Published
2010-02-00
Epub
2009-00-17
Pages
265-72
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC2813482
Subset
IM
External Links
PubMed source DOI: 10.1101/gr.097261.109 PMC Full Text View journal details
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