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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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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
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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
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QUAST: quality assessment tool for genome assemblies
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A human gut microbial gene catalogue established by metagenomic sequencing
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“UsingSOAPdenovo 19 ,adeBruijngraph-basedtoolspecially designed for assembling very short reads, we performed de novo assembly for all of the Illumina GA sequence data.”
MethodInfluentialSelf-citationSOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., Liu, Y., et al. (2012) · GigaScience · doi:10.1186/2047-217x-1-18 · Cited by 5,365
“The previous assembly was done using SOAPdenovo1 [3], but in addition it was also limited by the very short read lengths (~35 bp) that were the standard output of Illumina Genome Analyzers (GAIIx) at that time and by the insert sizes available (maximum size is 10 kb).”
BackgroundMethodInfluentialSelf-citationPeng, Y., Leung, H. C. M., Yiu, S., & Chin, F. Y. L. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts174 · Cited by 2,998
“To speed up the process, an error correction step is conducted to correct reads of high-depth regions that can be aligned to highconfident contigs.”
MethodAn integrated catalog of reference genes in the human gut microbiome
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Self-citationThe oyster genome reveals stress adaptation and complexity of shell formation
Zhang, G., Fang, X., Guo, X., Li, L., Luo, R., Xu, F., Yang, P., Zhang, L., Wang, X., Qi, H., et al. (2012) · Nature · doi:10.1038/nature11413 · Cited by 2,241
Self-citationAlterations of the human gut microbiome in liver cirrhosis
Qin, N., Yang, F., Li, A., Prifti, E., Chen, Y., Shao, L., Guo, J., Le Chatelier, E., Yao, J., Wu, L., et al. (2014) · Nature · doi:10.1038/nature13568 · Cited by 2,177
The genome of the mesopolyploid crop species Brassica rapa
Wang, X., Wang, H., Wang, J., Sun, R., Wu, J., Liu, S., Bai, Y., Mun, J., Bancroft, I., Cheng, F., et al. (2011) · Nature Genetics · doi:10.1038/ng.919 · Cited by 2,081
Self-citationGenome sequence and analysis of the tuber crop potato
Xu, X., Pan, S., Cheng, S., Zhang, B., Mu, D., Ni, P., Zhang, G., Guzman, F., Torres, M., Lozano, R., et al. (2011) · Nature · doi:10.1038/nature10158 · Cited by 2,050
Self-citationPhased diploid genome assembly with single-molecule real-time sequencing
Chin, C.-S., Peluso, P. S., Sedlazeck, F. J., Nattestad, M., Concepcion, G. T., Clum, A., Dunn, C., O’Malley, R. C., Figueroa-Balderas, R. E., Morales‐Cruz, A., et al. (2016) · Nature Methods · doi:10.1038/nmeth.4035 · Cited by 1,882
Genome structural variation discovery and genotyping
Alkan, C., Coe, B. P., & Eichler, E. E. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2958 · Cited by 1,630
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Self-citationDe novo assembly of bacterial transcriptomes from RNA-seq data
Tjaden, B. C. (2015) · Genome biology · doi:10.1186/s13059-014-0572-2 · Cited by 1,700
“In order to evaluate Rockhopper 2 ’ s performance, we compared it with two leading de novo transcriptome as-semblers: Trinity version trinityrnaseq_r20140413p1 [8,25] and SOAPdenovo2 version 2.04 [10,26].”
ResultInfluentialHigh-quality draft assemblies of mammalian genomes from massively parallel sequence data
Gnerre, S., MacCallum, I., Przybylski, D., Ribeiro, F. J., Burton, J. N., Walker, B. J., Sharpe, T., Hall, G., Shea, T., Sykes, S. M., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1017351108 · Cited by 1,510
“For example, the human scaffolds are >25 times longer than those in recently published assemblies using data from Illumina and 454 sequencing (12, 24).”
BackgroundMethodInfluentialChromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
Burton, J. N., Adey, A., Patwardhan, R. P., Qiu, R., Kitzman, J. O., & Shendure, J. (2013) · Nature Biotechnology · doi:10.1038/nbt.2727 · Cited by 1,470
“For example, the human genome was assembled with 40 gigabases (Gb) of Sanger sequencing, but de novo assemblies of short reads relying on five to tenfold more sequence are highly fragmented relative to the finished chromosomes of the H. sapiens reference build 6,7 .”
BackgroundZimin, A. V., Marçais, G., Puiu, D., Roberts, M., Salzberg, S. L., & Yorke, J. A. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt476 · Cited by 1,461
“…many reads as Sanger-sequencing projects; e.g. the original human (Lander et al., 2001; Venter et al., 2001) and mouse (Mouse Genome Sequencing Consortium et al., 2002) projects generated $35 million reads each, whereas recent human sequencing projects (Li et al., 2010) generated 3–4 billion reads.”
BackgroundPhylotranscriptomic analysis of the origin and early diversification of land plants
Wickett, N. J., Mirarab, S., Nguyen, N., Warnow, T., Carpenter, E., Matasci, N., Ayyampalayam, S., Barker, M. S., Burleigh, J. G., Gitzendanner, M. A., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1323926111 · Cited by 1,252
“RNA-Seq reads were assembled using SOAPdenovo v1 (111).”
MethodSelf-citationFunctional overlap of the Arabidopsis leaf and root microbiota
Bai, Y., Müller, D. B., Srinivas, G., Garrido‐Oter, R., Potthoff, E., Rott, M., Dombrowski, N., Münch, P. C., Spaepen, S., Remus‐Emsermann, M. N. P., et al. (2015) · Nature · doi:10.1038/nature16192 · Cited by 1,359
MetaHIT Consortium, Nielsen, H. B., Almeida, M., Juncker, A. S., Rasmussen, S., Li, J., Sunagawa, S., Plichta, D. R., Gautier, L., Pedersen, A. G., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2939 · Cited by 1,184
Self-citationAssembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products
Nurk, S., Bankevich, A., Antipov, D., Gurevich, A. A., Korobeynikov, A., Lapidus, A. L., Prjibelski, A. D., Pyshkin, A., Sirotkin, A., Sirotkin, Y., et al. (2013) · Journal of Computational Biology · doi:10.1089/cmb.2013.0084 · Cited by 1,352
“In particular, we show that it improves on A5 (Tritt et al., 2012), ABySS ASSEMBLING SINGLE CELL GENOMES AND MINI-METAGENOMES (Simpson et al., 2009), CLC, 1 EULER-SR (Chaisson et al., 2009), Ray (Boisvert et al., 2010), SOAPde-novo (Li et al., 2010), and Velvet (Zerbino and Birney, 2008) in multicell bacterial assembl…”
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
Self-citationAssembly algorithms for next-generation sequencing data
Miller, J. R., Koren, S., & Sutton, G. G. (2010) · Genomics · doi:10.1016/j.ygeno.2010.03.001 · Cited by 1,186
“The SOAPdenovo program [59] generated high-quality mammalian genome sequences from billions of Solexa reads of length 75 bp and less [60,61].”
Li, F., Fan, G., Lu, C., Xiao, G., Zou, C., Kohel, R. J., Ma, Z., Shāng, H., Ma, X., Wu, J., et al. (2015) · Nature Biotechnology · doi:10.1038/nbt.3208 · Cited by 1,119
Self-citationDNA sequencing at 40: past, present and future
Shendure, J., Balasubramanian, S., Church, G. M., Gilbert, W., Rogers, J., Schloss, J. A., & Waterston, R. (2017) · Nature · doi:10.1038/nature24286 · Cited by 1,166
Comparative genomics reveals insights into avian genome evolution and adaptation
Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., Storz, J. F., Antunes, A., Greenwold, M. J., Meredith, R. W., et al. (2014) · Science · doi:10.1126/science.1251385 · Cited by 1,055
Self-citationEfficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
Kajitani, R., Toshimoto, K., Noguchi, H., Toyoda, A., Ogura, Y., Okuno, M., Yabana, M., Harada, M., Nagayasu, E., Maruyama, H., et al. (2014) · Genome Research · doi:10.1101/gr.170720.113 · Cited by 1,017
Hybrid error correction and de novo assembly of single-molecule sequencing reads
Koren, S., Schatz, M. C., Walenz, B. P., Martin, J. V., Howard, J. T., Ganapathy, G., Wang, Z., Rasko, D. A., McCombie, W. R., Jarvis, E. D., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2280 · Cited by 1,025
“The baseline SOAPdenovo assembly (purple star) represents an assembly of 50× of real 76-bp Illumina paired-end (300 bp) reads from S. cerevisiae S228c.”
MethodThe draft genome of a diploid cotton Gossypium raimondii
Wang, K., Wang, Z., Li, F., Ye, W., Wang, J., Song, G., Yue, Z., Cong, L., Shāng, H., Zou, C., et al. (2012) · Nature Genetics · doi:10.1038/ng.2371 · Cited by 1,010
Self-citationThe draft genome of sweet orange (Citrus sinensis)
Xu, Q., Chen, L.-L., Ruan, X., Chen, D., Zhu, A., Chen, C., Bertrand, D., Jiao, W., Hao, B., Lyon, M. T., et al. (2012) · Nature Genetics · doi:10.1038/ng.2472 · Cited by 1,011
SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
Xie, Y., Wu, G., Tang, J., Luo, R., Patterson, J., Liu, S., Huang, W., He, G., Gu, S., Li, S., et al. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu077 · Cited by 1,012
Self-citationBertioli, D. J., Cannon, S. B., Froenicke, L., Huang, G., Farmer, A. D., Cannon, E. K. S., Liu, X., Gao, D., Clevenger, J. P., Dash, S., et al. (2016) · Nature Genetics · doi:10.1038/ng.3517 · Cited by 975
A window into third-generation sequencing
Schadt, E. E., Turner, S., & Kasarskis, A. (2010) · Human Molecular Genetics · doi:10.1093/hmg/ddq416 · Cited by 1,026
“genome repeat structure) to enhance assembly (53).”
A survey of sequence alignment algorithms for next-generation sequencing
Li, H., & Homer, N. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbq015 · Cited by 875
“Given a query AGC, for example, the path matching the query is [0, 6]! [3, 3]![5, 5]![1, 1].”
BackgroundMethodSequencing technologies and genome sequencing
Pareek, C. S., Smoczynski, R., & Tretyn, A. (2011) · Journal of Applied Genetics · doi:10.1007/s13353-011-0057-x · Cited by 868
“It is now possible to assemble de novo a large genome, a good example can be derived from the recent genome assembly of the giant panda (Li et al. 2010b) which utilized the only short reads provided by next-generation DNA sequencing.”
BackgroundMind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology
English, A. C., Richards, S., Han, Y., Wang, M., Vee, V., Qu, J., Qin, X., Muzny, D. M., Reid, J. G., Worley, K. C., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0047768 · Cited by 868
“Second-generation genome assemblies have been based on shorter read, massively parallel sequencing technologies and De Bruijn graph assembly techniques [12–15] Depending on the dataset quality, polymorphism, and repetitiveness of the target genome, both approaches generate draft genomes with contig N50 sizes ranging f…”
Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers
Varshney, R. K., Chen, W., Li, Y., Bharti, A. K., Saxena, R. K., Schlueter, J. A., Donoghue, M. T. A., Azam, S., Fan, G., Whaley, A. M., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.2022 · Cited by 890
Self-citationGenome sequence of the cultivated cotton Gossypium arboreum
Li, F., Fan, G., Wang, K., Sun, F., Yuán, Y., Song, G., Qin, L., Ma, Z., Lu, C., Zou, C., et al. (2014) · Nature Genetics · doi:10.1038/ng.2987 · Cited by 870
“5e ; see Supplementary Table 17 for primer sequences), we found that fiber-specific upregulation of ACO expression, as in the case of G. hirsutum , seems to be required for normal fiber growth.”
InfluentialSelf-citationGuo, J., Li, J., Chen, H., Bond, P. L., & Yuan, Z. (2017) · Water Research · doi:10.1016/j.watres.2017.07.002 · Cited by 862
“L 90 -u) (Li et al., 2010).”
Xu, X., Liu, X., Ge, S., Jensen, J. D., Hu, F., Li, X., Dong, Y., Gutenkunst, R. N., Fang, L., Huang, L., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.2050 · Cited by 845
“23, 578–587 (2007). 2.”
Self-citationChen, S., Zhang, G., Shao, C., Huang, Q., Liu, G., Zhang, P., Song, W., An, N., Chalopin, D., Volff, J., et al. (2014) · Nature Genetics · doi:10.1038/ng.2890 · Cited by 812
“We next assembled reads to contigs and scaffolds to build the male and female genomes using SOAPdenovo ( Supplementary Tables 2 and 3 ) 58 .”
Self-citationThe draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions
Guo, S., Zhang, J., Sun, H., Salse, J., Lucas, W. J., Zhang, H., Zheng, Y., Mao, L., Ren, Y., Wang, Z., et al. (2012) · Nature Genetics · doi:10.1038/ng.2470 · Cited by 818
Self-citationQin, C., Yu, C., Shen, Y., Fang, X., Chen, L., Min, J., Cheng, J., Zhao, S., Xu, M., Luo, Y., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1400975111 · Cited by 798
“Pair-end information was used sequentially in assembler SOAPdenovo (14) to generate scaffolds comprising 3.48- and 3.35-Gb scaffolds with N50 lengths of 1.23 Mb and 445 kb, respectively (Table 1 and SI Appendix, Table S4).”
MethodInfluentialSelf-citationZhang, G., Liu, X., Quan, Z., Cheng, S., Xu, X., Pan, S., Xie, M., Zeng, P., Yue, Z., Wang, W., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2195 · Cited by 794
Self-citationThe genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line
Xu, X., Nagarajan, H., Lewis, N. E., Pan, S., Cai, Z., Liu, X., Chen, W., Xie, M., Wang, W., Hammond, S., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1932 · Cited by 785
Self-citationEfficient de novo assembly of large genomes using compressed data structuresPreprint
Simpson, J. T., & Durbin, R. M. (2011) · Genome Research · doi:10.1101/gr.126953.111 · Cited by 767
“Currently available assemblers require either a single computer with very large amounts of memory—typically in the hundreds of gigabytes (Li et al. 2010b; Gnerre et al. 2011)—or a large distributed cluster of tightly coupled computers (Simpson et al. 2009; Boisvert et al. 2010).”
BackgroundMethodInfluentialNurk, S., Walenz, B. P., Rhie, A., Vollger, M. R., Logsdon, G. A., Grothe, R., Miga, K. H., Eichler, E. E., Phillippy, A. M., & Koren, S. (2020) · Genome Research · doi:10.1101/gr.263566.120 · Cited by 723
“This pipeline alignsreads usingminimap2 (Li 2018) and parsesthe SAM (Li et al. 2009) format to generate summary statistics.”
MethodDraft genome of the wheat A-genome progenitor Triticum urartu
Ling, H., Zhao, S., Liu, D., Wang, J., Sun, H., Zhang, C., 范华杰, Dong, L., Dong, L., Gao, C., et al. (2013) · Nature · doi:10.1038/nature11997 · Cited by 736
Self-citationLimitations of next-generation genome sequence assembly
Alkan, C., Sajjadian, S., & Eichler, E. E. (2010) · Nature Methods · doi:10.1038/nmeth.1527 · Cited by 754
Insights from 20 years of bacterial genome sequencing
Land, M., Hauser, L., Jun, S., Nookaew, I., Leuze, M. R., Ahn, T.-H., Karpinets, T. V., Lund, O., Kora, G., Wassenaar, T. M., et al. (2015) · Functional & Integrative Genomics · doi:10.1007/s10142-015-0433-4 · Cited by 771
“Another approach within an alignment-free category for whole genome and proteome comparison was proposed by Jun and colleagues (Li et al. 2010).”
BackgroundAegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation
Jia, J., Zhao, S., Kong, X., Li, Y., Zhao, G., He, W., Appels, R., Pfeifer, M., Tao, Y., Zhang, X., et al. (2013) · Nature · doi:10.1038/nature12028 · Cited by 725
Self-citationDe novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits
Li, Y., Zhou, G., Ma, J., Jiang, W., Jin, L., Zhang, Z., Guo, Y., Zhang, J., Sui, Y., Zheng, L., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2979 · Cited by 722
Self-citationPoretsky, R., Rodriguez-R, L. M., Luo, C., Tsementzi, D., & Konstantinidis, K. T. (2014) · PLoS ONE · doi:10.1371/journal.pone.0093827 · Cited by 684
“The reads were assembled into contigs as described previously [29]; Table S4 in File S1 using the SOAPdenovo [33] and Velvet [34] prefollowed by assembly into longer contigs with Newbler 2.”
MethodFisher, S., Barry, A. J., Abreu, J., Minie, B., Nolan, J., Delorey, T. M., Young, G., Fennell, T. J., Allen, A., Ambrogio, L., et al. (2011) · Genome biology · doi:10.1186/gb-2011-12-1-r1 · Cited by 676
“As a result, it has recently become feasible to sequence nontrivial numbers of whole human genomes [3,5-10].”
BackgroundGAGE: 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
Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads
Nurk, S., Bankevich, A., Antipov, D., Gurevich, A. A., Korobeynikov, A., Lapidus, A. L., Prjibelsky, A., Pyshkin, A., Sirotkin, A., Sirotkin, Y., et al. (2013) · Lecture notes in computer science · doi:10.1007/978-3-642-37195-0_13 · Cited by 683
“) In particular, we show that it improves on A5 [13], ABySS [14], CLC, EULER-SR [15], Ray [16], SOAPdenovo [17]), and Velvet [18] in multicell bacterial assemblies.”
BackgroundNamiki, T., Hachiya, T., Tanaka, H. L., & Sakakibara, Y. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks678 · Cited by 669
How to apply de Bruijn graphs to genome assembly
Compeau, P. E. C., Pevzner, P. A., & Tesler, G. (2011) · Nature Biotechnology · doi:10.1038/nbt.2023 · Cited by 673
“An approach for removing bulges from de Bruijn graphs was outlined 19 in 2004 and, with some variations, is used in most existing NGS assemblers (EULER-SR 20 , Velvet 21 , ALLPATHS 22 , ABySS 23 , SOAPdenovo 24 ).”
MethodGenome sequence and genetic diversity of the common carp, Cyprinus carpio
Xu, P., Zhang, X., Wang, X., Li, J.-T., Liu, G., Kuang, Y., Xu, J. H., Zheng, X., Ren, L., Wang, G., et al. (2014) · Nature Genetics · doi:10.1038/ng.3098 · Cited by 675
Self-citationFrancioli, L. C., Menelaou, A., Pulit, S. L., Elbers, C. C., Kloosterman, W. P., van Setten, J., Nijman, I. J., Renkens, I., de Bakker, P. I. W., van Dijk, F., et al. (2014) · Nature Genetics · doi:10.1038/ng.3021 · Cited by 651
Self-citationThe coffee genome provides insight into the convergent evolution of caffeine biosynthesis
Denœud, F., Carretero‐Paulet, L., Dereeper, A., Droc, G., Guyot, R., Pietrella, M., Zheng, C., Alberti, A., Anthony, F., Aprea, G., et al. (2014) · Science · doi:10.1126/science.1255274 · Cited by 666
Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly
Lam, E. T., Hastie, A. R., Lin, C. J., Ehrlich, D., Das, S. K., Austin, M. D., Deshpande, P., Cao, H., Nagarajan, N., Xiao, M., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2303 · Cited by 664
Multiple reference genomes and transcriptomes for Arabidopsis thaliana
Gan, X., Stegle, O., Behr, J., Steffen, J. G., Drewe, P., Hildebrand, K. L., Lyngsø, R. B., Schultheiß, S. J., Osborne, E. J., Sreedharan, V. T., et al. (2011) · Nature · doi:10.1038/nature10414 · Cited by 641
The tobacco genome sequence and its comparison with those of tomato and potato
Sierro, N., Battey, J. N. D., Ouadi, S., Bakaher, N., Bovet, L., Willig, A., Goepfert, S., Peitsch, M. C., & Ivanov, N. V. (2014) · Nature Communications · doi:10.1038/ncomms4833 · Cited by 641
De novo assembly and genotyping of variants using colored de Bruijn graphs
Iqbal, Z., Cáccamo, M., Turner, I., Flicek, P., & McVean, G. (2012) · Nature Genetics · doi:10.1038/ng.1028 · Cited by 652
“De Bruijn graphs, which represent overlap information in a set of DNA sequences, are widely used in genome assembly and underlie many popular algorithms, including AllPaths-LG 31 , SOAPdenovo 32 , Abyss 39 and Velvet 30,40 .”
BackgroundA beginner’s guide to eukaryotic genome annotation
Yandell, M., & Ence, D. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3174 · Cited by 588
“They can be assembled de novo — that is, independently of the genome — using tools such as ABySS 48 , SOAPdenovo 49 and Trinity 50 ; the resulting transcripts are then realigned to the genome in the same way as ESTs. Alternatively, the RNA-seq data can be directly aligned to the genome using tools…”
MethodFastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads
Xu, H., Luo, X., Qian, J., Pang, X., Song, J., Qian, G., Chen, J., & Chen, S. (2012) · PLoS ONE · doi:10.1371/journal.pone.0052249 · Cited by 602
“In general, a 64 GB memory is a minimum requirement for subsequent large-scale data analysis using popular tools such as Velvet [31], SOAPdenovo [32], ALLPATHS-LG [33] and so on.”
MethodWebMGA: a customizable web server for fast metagenomic sequence analysis
Wu, S., Zhu, Z., Fu, L., Niu, B., & Li, W. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-444 · Cited by 623
“…these problems, many meth-ods have been developed such as taxonomy binning [9-11], use of simulated datasets [12], diversity analysis [13], ORF calling [14,15], rRNA prediction [16], sequence clustering [17-20], assembly [21], statistical comparison [22], fragment recruitment [1,8,23] and so on.”
MethodComparative Analysis of Bat Genomes Provides Insight into the Evolution of Flight and Immunity
Zhang, G., Cowled, C. J., Shi, Z., Huang, Z., Bishop‐Lilly, K. A., Fang, X., Wynne, J. W., Xiong, Z., Baker, M. L., Zhao, W., et al. (2012) · Science · doi:10.1126/science.1230835 · Cited by 630
Self-citationThe Monarch Butterfly Genome Yields Insights into Long-Distance Migration
Zhan, S., Merlin, C., Boore, J. L., & Reppert, S. M. (2011) · Cell · doi:10.1016/j.cell.2011.09.052 · Cited by 597
“Remaining gaps within these scaffolds were iteratively filled with paired-end SIPES reads and the Roche 454 contigs using GapCloser available in SOAPdenovo (Li et al., 2010).”
Quake: quality-aware detection and correction of sequencing errors
Kelley, D. R., Schatz, M. C., & Salzberg, S. L. (2010) · Genome biology · doi:10.1186/gb-2010-11-11-r116 · Cited by 581
“A number of related methods have been proposed to perform this error correction step, all guided by the goal of finding the minimum number of single base edits (edit distance) to the read that make all k-mers trusted [11-14].”
BackgroundMethodInfluentialThe impact of next-generation sequencing on genomics
Zhang, J., Chiodini, R., Badr, A., & Zhang, G. (2011) · Journal of Genetics and Genomics · doi:10.1016/j.jgg.2011.02.003 · Cited by 577
“Individual human genomes (one Asian and one African) have been successfully sequenced and assembled using the Illumina Genome Analyzer (read lengths ranged from 35 to 75 basepairs) with a modified SOAP program, SOAPdenovo (Li et al., 2010).”
MethodThe draft genome and transcriptome of Cannabis sativa.
van Bakel, H., Stout, J. M., Cote, A. G., Tallon, C. M., Sharpe, A. G., Hughes, T. R., & Page, J. E. (2011) · Genome Biology · doi:10.1186/gb-2011-12-10-r102 · Cited by 575
“We used different approaches for the de novo assembly of the PK genome (SOAPdenovo [25]) and transcriptome (ABySS [26] and Inchworm [27]).”
MethodGenomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars
Li, M., Tian, S., Jin, L. G., Zhou, G., Li, Y., Zhang, Y., Wang, T., Yeung, C. K. L., Chen, L., Ma, J., et al. (2013) · Nature Genetics · doi:10.1038/ng.2811 · Cited by 560
Self-citationA reference genome for pea provides insight into legume genome evolution
Kreplak, J., Madoui, M., Cápal, P., Novák, P., Labadie, K., Aubert, G., Bayer, P. E., Gali, K. K., Syme, R. A., Main, D., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0480-1 · Cited by 573
The locust genome provides insight into swarm formation and long-distance flight
Wang, X., Fang, X., Yang, P., Jiang, X., Jiang, F., Zhao, D., Li, B., Cui, F., Wei, J., Ma, C., et al. (2014) · Nature Communications · doi:10.1038/ncomms3957 · Cited by 544
Self-citationDong, Y., Xie, M., Jiang, Y., Xiao, N., Du, X., Zhang, W., Tosser‐Klopp, G., Wang, J., Yang, S., Liang, J., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2478 · Cited by 531
Self-citationScheinin, I., Sie, D., Bengtsson, H. L., van de Wiel, M. A., Olshen, A. B., van Thuijl, H. F., Essen, H. F. H. V., Eijk, P. P., Rustenburg, F., Meijer, G. A., et al. (2014) · Genome Research · doi:10.1101/gr.175141.114 · Cited by 497
Qi, J., Liu, X., Shen, D., Miao, H., Xie, B., Li, X., Zeng, P., Wang, S., Shang, Y., Gu, X., et al. (2013) · Nature Genetics · doi:10.1038/ng.2801 · Cited by 523
Self-citationA genome triplication associated with early diversification of the core eudicots
Jiao, Y., Leebens‐Mack, J., Ayyampalayam, S., Bowers, J., McKain, M. R., McNeal, J. R., Rolf, M., Ruzicka, D. R., Wafula, E. K., Wickett, N. J., et al. (2012) · Genome biology · doi:10.1186/gb-2012-13-1-r3 · Cited by 520
“Short-read Illumina datasets were assembled either with SOAP denovo (Kmer size = 29 and asm_flag = 2) [67] or with CLC Genomics Workbench (reads trimmed first, and using default parameters except minimum contig length set to 200 bases).”
MethodSelf-citationNagarajan, N., & Pop, M. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3367 · Cited by 474
“This approach was extended to the assembly of large genomes in the program ABySS 21 and for the first de novo assembly of a mammalian genome entirely using short reads with the program SOAPdenovo 22 .”
MethodInfluentialEvidence of cellulose metabolism by the giant panda gut microbiome
Zhu, L., Wu, Q., Dai, J., Zhang, S., & Wei, F. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1017956108 · Cited by 509
“The de novo assembly (22) for Illumina Genome Analyzer sequence data resulted in a set of ∼37 Mbp (SI Appendix, Table S4).”
MethodPearl millet genome sequence provides a resource to improve agronomic traits in arid environments
Varshney, R. K., Shi, C., Thudi, M., Mariac, C., Wallace, J. G., Qi, P., Zhang, H., Zhao, Y., Wang, X., Rathore, A., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3943 · Cited by 528
Self-citationproovread : large-scale high-accuracy PacBio correction through iterative short read consensus
Hackl, T., Hedrich, R., Schultz, J., & Förster, F. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu392 · Cited by 510
“Accordingly, a plenitude of short read assemblers has been developed, e.g. Allpath-LG (Gnerre et al., 2011), the Celera Assembler (Myers et al., 2000; Miller et al., 2008), and SOAPdenovo (R. Li et al., 2010).”
MethodDraft genome of the kiwifruit Actinidia chinensis
Huang, S., Ding, J. H., Deng, D., Tang, W. D., Sun, H., Liu, D., Zhang, L., Niu, X., Zhang, X., Meng, M., et al. (2013) · Nature Communications · doi:10.1038/ncomms3640 · Cited by 517
Assemblathon 1: A competitive assessment of de novo short read assembly methodsPreprint
Earl, D. A., Bradnam, K. R., John, J. S., Darling, A. E., Lin, D., Fass, J., Yu, H. O. K., Buffalo, V., Zerbino, D. R., Diekhans, M., et al. (2011) · Genome Research · doi:10.1101/gr.126599.111 · Cited by 525
Self-citationBile acid metabolism and signaling, the microbiota, and metabolic disease
Cai, J., Rimal, B., Jiang, C., Chiang, J. Y. L., & Patterson, A. D. (2022) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2022.108238 · Cited by 529
The genome sequence of the orchid Phalaenopsis equestris
Cai, J., Liu, X., Vanneste, K., Proost, S., Tsai, W., Liu, K., Chen, L., He, Y., Xu, Q., Bian, C., et al. (2014) · Nature Genetics · doi:10.1038/ng.3149 · Cited by 507
Self-citationMetagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis
Aguiar‐Pulido, V., Huang, W., Suárez-Ulloa, V., Cickovski, T., Mathee, K., & Narasimhan, G. (2016) · Evolutionary Bioinformatics · doi:10.4137/ebo.s36436 · Cited by 549
Assembly of large genomes using second-generation sequencingPreprint
Schatz, M. C., Delcher, A. L., & Salzberg, S. L. (2010) · Genome Research · doi:10.1101/gr.101360.109 · Cited by 518
Ultrafast clustering algorithms for metagenomic sequence analysis
Li, W., Fu, L., Niu, B., Wu, S., & Wooley, J. (2012) · Briefings in Bioinformatics · doi:10.1093/bib/bbs035 · Cited by 498
“The comparison of contigs between original reads and filtered reads using Velvet [63] and SOAPdenovo [64] is shown in Figure 2.”
MethodUsing the Velvet de novo Assembler for Short‐Read Sequencing Technologies
Zerbino, D. R. (2010) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1105s31 · Cited by 494
“Velvet does not allow you to directly measure this k -mer coverage, but you can use tallymer (Kurtz et al., 2008) to produce this distribution.”
MethodMace, E., Tai, S., Gilding, E. K., Li, Y., Prentis, P. J., Bian, L., Campbell, B. C., Hu, W., Innes, D. J., Han, X., et al. (2013) · Nature Communications · doi:10.1038/ncomms3320 · Cited by 509
“Unmapped reads from each sample were assembled into contigs using SOAPdenovo 50 (default parameters).”
Self-citationZhang, Q., Chen, W., Sun, L., Zhao, F., Huang, B., Yang, W., Tao, Y., Wang, J., Yuan, Z., Fan, G., et al. (2012) · Nature Communications · doi:10.1038/ncomms2290 · Cited by 493
Self-citationA roadmap for natural product discovery based on large-scale genomics and metabolomics
Doroghazi, J. R., Albright, J. C., Goering, A. W., Ju, K., Haines, R. R., Tchalukov, K., Labeda, D. P., Kelleher, N. L., & Metcalf, W. W. (2014) · Nature Chemical Biology · doi:10.1038/nchembio.1659 · Cited by 485
Genome-wide patterns of genetic variation among elite maize inbred lines
Lai, J., Li, R., Xu, X., Jin, W., Xu, M., Zhao, H., Xiang, Z., Song, W., Ying, K., Zhang, M., et al. (2010) · Nature Genetics · doi:10.1038/ng.684 · Cited by 473
Self-citationChen, H., Zeng, Y., Yang, Y. P., Huang, L., Tang, B., Zhang, H., Hao, F., Liu, W., Li, Y., Liu, Y., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16338-x · Cited by 481
Self-citationLuo, C., Tsementzi, D., Kyrpides, N. C., Read, T. D., & Konstantinidis, K. T. (2012) · PLoS ONE · doi:10.1371/journal.pone.0030087 · Cited by 481
“We performed six independent assemblies, using K = 21, 25, 29 for the three PLoS ONE | www.plosone.org 8 February 2012 | Volume 7 | Issue 2 | e30087 SOAPdenovo runs and K = 23, 27, 31 for the three Velvet runs.”
Method
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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