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

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

ContigSequence assemblyBiologyMassive parallel sequencingHybrid genome assemblyMassively parallelGenomeDNA sequencingComputational biologyHuman genomeReference genomeGeneticsDNAComputer scienceGeneParallel computingTranscriptome

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Publication Info

Year: 2009
Type: article
Volume: 20
Issue: 2
Pages: 265-272
Citations: 2939
Access: Closed

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APA Style

                            
                                
                                    Ruiqiang Li, 
                                
                                    Hongmei Zhu, 
                                
                                    Jue Ruan
                                
                                et al.
                            
                            (2009). 
                            De novo assembly of human genomes with massively parallel short read sequencing. 
                            Genome Research
                            , 20
                            (2)
                            , 265-272.
                            https://doi.org/10.1101/gr.097261.109
                        

Identifiers

DOI: 10.1101/gr.097261.109