De novo assembly of human genomes with massively parallel short read sequencing
Top Cited Papers
Open Access
- 17 December 2009
- journal article
- Published by Cold Spring Harbor Laboratory in Genome Research
- Vol. 20 (2) , 265-272
- https://doi.org/10.1101/gr.097261.109
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.Keywords
This publication has 32 references indexed in Scilit:
- SOAP2: an improved ultrafast tool for short read alignmentBioinformatics, 2009
- Accurate whole human genome sequencing using reversible terminator chemistryNature, 2008
- The diploid genome sequence of an Asian individualNature, 2008
- Mapping and sequencing of structural variation from eight human genomesNature, 2008
- SOAP: short oligonucleotide alignment programBioinformatics, 2008
- A second generation human haplotype map of over 3.1 million SNPsNature, 2007
- SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencingGenome Research, 2007
- Advanced sequencing technologies: methods and goalsNature Reviews Genetics, 2004
- Initial sequencing and comparative analysis of the mouse genomeNature, 2002
- Initial sequencing and analysis of the human genomeNature, 2001