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De novo assembly of human genomes with massively parallel short read sequencing
Open accessAbstract
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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“The newly developed high throughput sequencing technology, i.e. Next Generation Sequencing (NGS), including the Roche/454 Genome Sequencer FLX Instrument, the ABI SOLiD System, and the Illumina Genome Analyser, is a powerful and cost-efficient tool for advanced research in many areas, including re-sequencing, microRNA expression profiling, DNA methylation, especially de novo transcriptome”
From De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas) (2010) · cites this paper as [16]
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“Over the last two years, with the further confirmation that the relatively short reads can be effectively assembled [15], especially with the great advantage of paired-end sequencing [54], the Illumina transcriptome or whole genome de novo sequencing and assembly have been successfully used for model [12,16,55-58]and non-model organisms [25-27,59].”
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“The final assembly output was also much better than the recent study on sweet potato root transcriptome, which was assembled with the SOAPdenovo software [53].”
From Digital Gene Expression Analysis Based on Integrated De Novo Transcriptome Assembly of Sweet Potato [Ipomoea batatas (L.) Lam.] (2012) · cites this paper as [53]
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“gene 1465 of Bacteroides ovatus encoded HsdR family type I site-specific deoxyribonuclease, which can digest DNA to produce monodeoxynucleotides.31”
From Gut microbiota drives structural variation of exogenous probiotics to enhance colonization (2025) · cites this paper as [31]
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Citations
Cites
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
The sequence of the human genome
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909
Self-citationVelvet: Algorithms for de novo short read assembly using de Bruijn graphsPreprint
Zerbino, D. R., & Birney, E. (2008) · Genome Research · doi:10.1101/gr.074492.107 · Cited by 9,587 · cited 5×
“In our method, we used a similar de Bruijn graph data structure as Velvet (Zerbino and Birney 2008), but we did not record the read locations and paired-end information in the graph as is done in Velvet.”
MethodInfluentialInitial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
A second generation human haplotype map of over 3.1 million SNPs
The International HapMap Consortium (2007) · Nature · doi:10.1038/nature06258 · Cited by 4,438 · cited 2×
“This maybe due to the Asian genome assembly having a longer total length, and may also be because the Asian genome is more similar to the NCBI reference genome than is the African genome (International HapMap Consortium 2007; Bentley et al. 2008; Wang et al. 2008).”
MethodSOAP2: an improved ultrafast tool for short read alignment
Li, R., Yu, C., Li, Y., Lam, T., Yiu, S., Kristiansen, K., & Wang, J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp336 · Cited by 3,763
Self-citationAccurate whole human genome sequencing using reversible terminator chemistry
Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684 · cited 10×
“%) chimeric reads in long paired-end ( $ 2 kb) sequencing are generated in the circularizing and fragmentation process (Bentley et al. 2008), we only used single-end and paired-end reads with insert sizes of 140 bp and 440 bp for contig assembly; all paired-end data were used for scaffold…”
BackgroundMethodResultInfluentialSelf-citationABySS: A parallel assembler for short read sequence dataPreprint
Simpson, J. T., Wong, K., Jackman, S. D., Schein, J. E., Jones, S. J. M., & Birol, İ. (2009) · Genome Research · doi:10.1101/gr.089532.108 · Cited by 3,658
SOAP: Short oligonucleotide alignment program
Li, R., Li, Y., Kristiansen, K., & Wang, J. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn025 · Cited by 3,597 · cited 11×
“SOAPdenovo reported 182 contigs ( > 100 bp in length), with mean size of 25 kb and N50 size of 89 kb, and only five incorrect contigs, which indicated both longer contig size and assembly accuracy than the others.”
MethodInfluentialSelf-citationThe Sequence of the Human Genome
Venter, J. C., Smith, H. O., & Adams, M. D. (2015) · Clinical Chemistry · doi:10.1373/clinchem.2014.237016 · Cited by 1,665
A Whole-Genome Assembly of Drosophila
Myers, E. W., Sutton, G. G., Delcher, A. L., Dew, I. M., Fasulo, D., Flanigan, M. J., Kravitz, S. A., Mobarry, C. M., Reinert, K., Remington, K., et al. (2000) · Science · doi:10.1126/science.287.5461.2196 · Cited by 1,533
The genome of the cucumber,Cucumis sativus L
Huang, S., Li, R., Zhang, Z., Li, L., Gu, X., Fan, W., Lucas, W. J., Wang, X., Xie, B., Ni, P., et al. (2009) · Nature Genetics · doi:10.1038/ng.475 · Cited by 1,490 · cited 1×
“Currently, using the Illumina GA sequencing technology and our short read as-sembler presented here, we have sequenced and assembled nearly a dozen plant and animal genomes, including the panda (Li et al. 2009d), duck, potato, cucumber (Huang et al. 2009), watermelon, and others.”
MethodSelf-citationAn Eulerian path approach to DNA fragment assembly
Pevzner, P. A., Tang, H., & Waterman, M. S. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.171285098 · Cited by 1,352
The sequence and de novo assembly of the giant panda genome
Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., Huang, Q., Cai, Q., Li, B., Bai, Y., et al. (2010) · Nature · doi:10.1038/nature08696 · Cited by 1,180 · cited 13×
“SOAPdenovo reported 182 contigs ( > 100 bp in length), with mean size of 25 kb and N50 size of 89 kb, and only five incorrect contigs, which indicated both longer contig size and assembly accuracy than the others.”
MethodInfluentialSelf-citationMapping and sequencing of structural variation from eight human genomes
Kidd, J. M., Cooper, G. M., Donahue, W. F., Hayden, H. S., Sampas, N., Graves, T., Hansen, N., Teague, B., Alkan, C., Antonacci, F., et al. (2008) · Nature · doi:10.1038/nature06862 · Cited by 1,119
SNP detection for massively parallel whole-genome resequencing
Li, R., Li, Y., Fang, X., Yang, H., Wang, J., Kristiansen, K., & Wang, J. (2009) · Genome Research · doi:10.1101/gr.088013.108 · Cited by 944
Self-citationThe diploid genome sequence of an Asian individual
Wang, J., Wang, W., Li, R., Li, Y., Tian, G., Goodman, L., Fan, W., Zhang, J., Li, J., Zhang, J., et al. (2008) · Nature · doi:10.1038/nature07484 · Cited by 924
Self-citationALLPATHS: De novo assembly of whole-genome shotgun microreadsPreprint
Butler, J., MacCallum, I., Kleber, M., Shlyakhter, I. A., Belmonte, M. K., Lander, E. S., Nusbaum, C., & Jaffe, D. B. (2008) · Genome Research · doi:10.1101/gr.7337908 · Cited by 823 · cited 1×
“A few short read assemblers, including Velvet (Zerbino and Birney 2008), ALLPATHS (Butler et al. 2008), and EULER-SR (Chaisson and Pevzner 2008), have adopted this algorithm, explicitly or implicitly, and have been implemented and shown very promising performances.”
MethodBentley, D. (2006) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2006.10.009 · Cited by 805 · cited 1×
“The development and commercialization of next-generation massively parallel DNA sequencing technologies, including Illumina Genome Analyzer (GA) (Bentley 2006), Applied Biosystems SOLiD System, and Helicos BioSciences HeliScope (Harris et al. 2008), have revolutionized genomic research.”
MethodGAGE: A critical evaluation of genome assemblies and assembly algorithmsPreprint
Salzberg, S. L., Phillippy, A. M., Zimin, A. V., Puiu, D., Magoč, T., Koren, S., Treangen, T. J., Schatz, M. C., Delcher, A. L., Roberts, M., et al. (2011) · Genome Research · doi:10.1101/gr.131383.111 · Cited by 706
Single-Molecule DNA Sequencing of a Viral Genome
Harris, T. D., Buzby, P. R., Babcock, H. P., Beer, E., Bowers, J., Braslavsky, I., Causey, M., Colonell, J. I., Dimeo, J. J., Efcavitch, J. W., et al. (2008) · Science · doi:10.1126/science.1150427 · Cited by 703 · cited 1×
“The development and commercialization of next-generation massively parallel DNA sequencing technologies, including Illumina Genome Analyzer (GA) (Bentley 2006), Applied Biosystems SOLiD System, and Helicos BioSciences HeliScope (Harris et al. 2008), have revolutionized genomic research.”
MethodDe novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computerPreprint
Hernández, D., François, P., Farinelli, L., Østerås, M., & Schrenzel, J. (2008) · Genome Research · doi:10.1101/gr.072033.107 · Cited by 632 · cited 3×
“…size of E. coli library (SRX000429); the other assemblers, including ABySS (Simpson et al. 2009), Velvet (Zerbino and Birney 2008), EULER-SR (Chaisson and Pevzner 2008), SSAKE (Warren et al. 2007), and Edena (Hernandez et al. 2008), have been evaluated using this data set (Simpson et al. 2009).”
MethodInfluentialHigh-Throughput Gene Mapping in Caenorhabditis elegansPreprint
Swan, K. A., Curtis, D. E., McKusick, K. B., Voinov, A. V., Mapa, F., & Cancilla, M. R. (2002) · Genome Research · doi:10.1101/gr.208902 · Cited by 617
Advanced sequencing technologies: methods and goals
Shendure, J., Mitra, R. D., Varma, C., & Church, G. M. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1325 · Cited by 569
Assembling millions of short DNA sequences using SSAKE
Warren, R. M., Sutton, G. G., Jones, S. J. M., & Holt, R. A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl629 · Cited by 497
Short read fragment assembly of bacterial genomesPreprint
Chaisson, M., & Pevzner, P. A. (2007) · Genome Research · doi:10.1101/gr.7088808 · Cited by 444 · cited 3×
“A few short read assemblers, including Velvet (Zerbino and Birney 2008), ALLPATHS (Butler et al. 2008), and EULER-SR (Chaisson and Pevzner 2008), have adopted this algorithm, explicitly or implicitly, and have been implemented and shown very promising performances.”
MethodInfluentialPCAP: A Whole-Genome Assembly ProgramPreprint
Huang, X., Wang, J., Aluru, S., Yang, S., & Hillier, L. (2003) · Genome Research · doi:10.1101/gr.1390403 · Cited by 289 · cited 2×
“Several programs, such as phrap (http://www.phrap.org), Celera assembler (Myers et al. 2000), ARACHNE (Batzoglou et al. 2002), Phusion (Mullikin and Ning 2003), RePS (Wang et al. 2002), PCAP (Huang et al. 2003), and Atlas (Havlak et al. 2004), have been successfully used for de novo assembly of whole-genome shotgun (W…”
MethodSelf-citationSHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencingPreprint
Dohm, J., Lottaz, C., Borodina, T., & Himmelbauer, H. (2007) · Genome Research · doi:10.1101/gr.6435207 · Cited by 281 · cited 1×
“Some other short read assemblers have applied the overlap and extension strategy, such as SSAKE (Warren et al. 2007), VCAKE (Jeck et al. 2007) (the follower of SSAKE which can handle sequencing errors), SHARCGS (Dohm et al. 2007), and Edena (Hernandez et al. 2008).”
MethodExtending assembly of short DNA sequences to handle error
Jeck, W. R., Reinhardt, J. A., Baltrus, D. A., Hickenbotham, M. T., Magrini, V. J., Mardis, E. R., Dangl, J. L., & Jones, C. D. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm451 · Cited by 269
Building the sequence map of the human pan-genome
Li, R., Li, Y., Zheng, H., Luo, R., Zhu, H., Li, Q., Qian, W., Ren, Y., Tian, G., Li, J., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1596 · Cited by 261
Self-citationMullikin, J. C., & Ning, Z. (2003) · Genome Research · doi:10.1101/gr.731003 · Cited by 222
The Atlas Genome Assembly SystemPreprint
Havlak, P., Chen, R., Durbin, K. J., Egan, A., Ren, Y., Song, X., Weinstock, G. M., & Gibbs, R. A. (2004) · Genome Research · doi:10.1101/gr.2264004 · Cited by 183
RePS: A Sequence Assembler That Masks Exact Repeats Identified from the Shotgun DataPreprint
Wang, J., Wong, G. K., Ni, P., Han, Y., Huang, X., Zhang, J., Ye, C., Zhang, Y., Hu, J., Zhang, K., et al. (2002) · Genome Research · doi:10.1101/gr.165102 · Cited by 72
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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M. V., Kulikov, A. S., Lesin, V. M., Nikolenko, S., Pham, S., Prjibelski, A. D., et al. (2012) · Journal of Computational Biology · doi:10.1089/cmb.2012.0021 · Cited by 26,312
Comprehensive Integration of Single-Cell Data
Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W. M., Hao, Y., Stoeckius, M., Smibert, P., & Satija, R. (2019) · Cell · doi:10.1016/j.cell.2019.05.031 · Cited by 15,453
FLASH: fast length adjustment of short reads to improve genome assemblies
Magoč, T., & Salzberg, S. L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr507 · Cited by 15,366
“Anyincreaseinreadlength willhaveasignificant,positiveimpactonthequalityofgenome assemblies. library of DNAfragments.”
QUAST: quality assessment tool for genome assemblies
Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt086 · Cited by 11,172
A human gut microbial gene catalogue established by metagenomic sequencing
MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624
“UsingSOAPdenovo 19 ,adeBruijngraph-basedtoolspecially designed for assembling very short reads, we performed de novo assembly for all of the Illumina GA sequence data.”
MethodInfluentialSelf-citation
Metadata
- Authors
- 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.
- Affiliations
- BGI Group (China) (CN)
- ORCID
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2009-12-17
- Volume
- 20
- Issue
- 2
- Pages
- 265-272
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC2813482
- OpenAlex
- W2161546116
- Cited by
- 2,926
- References
- 33
- Citations by year
- 2026: 48 · 2025: 79 · 2024: 105 · 2023: 101 · 2022: 139 · 2021: 177 · 2020: 190 · 2019: 217 · 2018: 150 · 2017: 205 · 2016: 229 · 2015: 244 · 2014: 261 · 2013: 289 · 2012: 292
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- Funders
- National Natural Science Foundation of China (30890032, 90608010, 30725008)
- National High-tech Research and Development Program
- National Key Research and Development Program of China (2007CB815705, 2007CB815703, 2007CB815701)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Mathematics › Theoretical Computer Science › Algorithms and Data Compression
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- de novo genome assembly, human genome, short-read sequencing, next-generation sequencing
- MeSH terms
- Humans, Genome, Human, Human Genome Project, Sequence Alignment, Sequence Analysis, DNA, Oligonucleotide Array Sequence Analysis, Black People, Asian People
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