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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
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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
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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
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“%) 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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Dong, Y., Zhang, X., Xie, M., Arefnezhad, B., Wang, Z., Wang, W., Feng, S., Huang, G., Guan, R., Shen, W., et al. (2015) · BMC Genomics · doi:10.1186/s12864-015-1606-1 · Cited by 116
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“With the 17-mer analysis model [31], the peak of the 17-mer distributed at 22, and the K-mer frequencies along the sequencing depth gradient followed a Poisson distribution.”
BackgroundMethodInfluentialSelf-citationDong, L., Xu, J., Zhang, L., Wei, G., Su, H., Yang, J., Qian, J., 徐冉, Liao, B., Chen, S., et al. (2018) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2017.12.011 · Cited by 116
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Self-citationZhao, X., Wang, Q., Jiao, Y., Huang, R., Deng, Y., Wang, H., & Du, X. (2012) · Marine Biotechnology · doi:10.1007/s10126-012-9438-3 · Cited by 114
Li, C., Wang, Y., Huang, X., Li, J., Wang, H., & Li, J. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-552 · Cited by 114
“html) [73] at the parameters of “-K 29 -M 2 -L 50” by BGI.”
Using SOAPaligner for Short Reads Alignment
Gu, S., Fang, L., & Xu, X. (2013) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1111s44 · Cited by 113
“Currently, the abbreviation SOAP represents Short Oligonucleotide Analysis Pack-age ( http://soap.genomics.org.cn/ ), consisting of an alignment tool, SOAPaligner, a re-sequencing consensus sequence builder, SOAPsnp (Li, R. et al., 2009a), an indel finder, SOAPindel (Li, S. et al., 2013), a structural variation (SV) sc…”
BackgroundHuman genetics and genomics a decade after the release of the draft sequence of the human genome
Naidoo, N., Yudi Pawitan, Y., Soong, R., Cooper, D. N., & Ku, C. (2011) · Human Genomics · doi:10.1186/1479-7364-5-6-577 · Cited by 117
“Recent studies have attempted to perform de novo human genome assembly using short sequence reads, with limited success.(291,310,311) One such study showed that de novo assemblies were 16.”
BackgroundDong, Y., Chen, R., Graham, E. B., Yu, B., Bao, Y., Li, X., You, X., & Feng, Y. (2024) · Nature Communications · doi:10.1038/s41467-024-50368-z · Cited by 117
Rondeau, E. B., Messmer, A., Sanderson, D. S., Jantzen, S. G., von Schalburg, K. R., Minkley, D. R., Leong, J. S., Macdonald, G. M., Davidsen, A. E., Parker, W. A., et al. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-452 · Cited by 109
“One lane of RNAseq 100 bp PET Illumina sequencing was run on a HiSeq2000 sequencer, and assembled using SOAPdenovo (k=75) [62]; sequencing was performed at the Beijing Genomics Institute.”
Wang, X., Luan, J., Li, J., Su, Y., Xia, J., & Liu, S. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-458 · Cited by 112
“These raw reads were assembled using SOAPdenovo software and resulted in 123,055 contigs (Table 1) [42].”
MethodDonkey genomes provide new insights into domestication and selection for coat color
Wang, C., Li, H., Guo, Y., Huang, J., Sun, Y., Min, J., Wang, J., Fang, X., Zhao, Z., Wang, S., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19813-7 · Cited by 115
Self-citationTranscriptional profile of Taxus chinensis cells in response to methyl jasmonate
Li, S.-T., Zhang, P., Zhang, M., Fu, C., Zhao, C., Dong, Y., Guo, A., & Yu, L. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-295 · Cited by 110
“Transcriptome de novo assembly was carried out with short reads assembling program SOAPdenovo which applies de Bruijn graph algorithm [18].”
BackgroundMethodSelf-citationState of the art de novo assembly of human genomes from massively parallel sequencing data
Li, Y., Hu, Y., Bolund, L., & Wang, J. (2010) · Human Genomics · doi:10.1186/1479-7364-4-4-271 · Cited by 110
Self-citationLiu, L., Xiao, J., Xia, X., Pan, Y., Yan, S., & Wang, Y. (2015) · Genome Announcements · doi:10.1128/genomea.01395-15 · Cited by 110
Evidence for horizontal transfer of mitochondrial DNA to the plastid genome in a bamboo genus
Ma, P., Zhang, Y., Guo, Z., & Li, D.-Z. (2015) · Scientific Reports · doi:10.1038/srep11608 · Cited by 110
Genome structure of Rosa multiflora, a wild ancestor of cultivated roses
Nakamura, N., Hirakawa, H., Sato, S., Otagaki, S., Matsumoto, S., Tabata, S., & Tanaka, Y. (2017) · DNA Research · doi:10.1093/dnares/dsx042 · Cited by 114
Lin, P., Wang, K., Zhou, C., Xie, Y., Yao, X., & Yin, H. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19010118 · Cited by 113
“The reads of the 4 stages were separately assembled into contigs, then unigenes using SOAP de novo software [54].”
MethodSOAPindel: Efficient identification of indels from short paired readsPreprint
Li, S., Li, R., Li, H., Lu, J., Li, Y., Bolund, L., Schierup, M. H., & Wang, J. (2012) · Genome Research · doi:10.1101/gr.132480.111 · Cited by 111
“As in most other de novo assembly algorithms (Li et al. 2010), we use a K-dimensional De Bruijn graph of four symbols (A|T|G|C) to store possible paths among K-mer vertices for each candidate region.”
MethodSelf-citationCorrection of sequencing errors in a mixed set of reads
Salmela, L. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq151 · Cited by 109
“This approach has been used with Examples of such tools are MisEd (”
MethodDe novo assembly of maritime pine transcriptome: implications for forest breeding and biotechnology
Canales, J., Bautista, R., Label, P., Maldonado, J. G., Lesur, I., Fernández‐Pozo, N., Rueda‐López, M., Guerrero-Fernández, D., Castro‐Rodríguez, V., Benzekri, H., et al. (2013) · Plant Biotechnology Journal · doi:10.1111/pbi.12136 · Cited by 108
Yu, X., Jin, T., Cui, Y., Pu, X., Li, J., Xu, J. H., Liu, G., Jia, H., Liu, D., Song, S., et al. (2014) · Journal of Virology · doi:10.1128/jvi.02059-13 · Cited by 108
Self-citationOral insecticidal activity of plant‐associated pseudomonads
Ruffner, B., Péchy‐Tarr, M., Ryffel, F., Hoegger, P. J., Obrist, C., Rindlisbacher, A., Keel, C., & Maurhofer, M. (2012) · Environmental Microbiology · doi:10.1111/j.1462-2920.2012.02884.x · Cited by 108
“05 after adjusting the K-mer size (Li et al., 2010).”
MethodInfluentialThe Genome of Ganderma lucidum Provide Insights into Triterpense Biosynthesis and Wood Degradation
Liu, D., Gong, J., Dai, W., Kang, X., Huang, Z., Zhang, H.-M., Liu, W., Liu, L., Ma, J., Xia, Z., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0036146 · Cited by 108
“The assembly was performed by SOAPdenovo genome assembler [22], firstly generated 1,724 contigs with N50 of 80,796 base pairs (bp) and then assembled into 634 scaffolds with N50 of 322,982 bp.”
MethodCarrotDB: a genomic and transcriptomic database for carrot
Xu, Z., Tan, H., Wang, F., Hou, X., & Xiong, A. (2014) · Database · doi:10.1093/database/bau096 · Cited by 108
“html) (7) and Newbler Assembler software (http:// swes.”
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Wang, S., Wang, X., He, Q., Liu, X., Xu, W., Li, L., Gao, J., & Wang, F. (2012) · Plant Cell Reports · doi:10.1007/s00299-012-1259-3 · Cited by 107
The Origins and Vulnerabilities of Two Transmissible Cancers in Tasmanian Devils
Stammnitz, M. R., Coorens, T. H. H., Gori, K. C., Hayes, D., Fu, B., Wang, J., Martin-Herranz, D. E., Alexandrov, L. B., Baez‐Ortega, A., Barthorpe, S., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.03.013 · Cited by 107
“SOAPdenovo (Li et al., 2010) was used to process the cleaned reads in a third assembly run, which was improved using SSPACE (Boetzer et al.”
BackgroundMethodSelf-citationMethods to improve the accuracy of next-generation sequencing
Cheng, C., Fei, Z., & Xiao, P. (2023) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2023.982111 · Cited by 111
“, 2011), SOAPdenovo (Li et al., 2010), and EDAR (Zhao et al.”
BackgroundJi, R., Yu, H., Fu, Q., Chen, H., Ye, W., Li, S., & Lou, Y. (2013) · PLoS ONE · doi:10.1371/journal.pone.0079612 · Cited by 106
“After the removal of empty and low-quality reads with undetermined nucleotides (‘N’), processed reads were assembled using SOAPdenovo software and clustered with TGI Clustering tools [76,77].”
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Transcriptomic Analysis of the Salivary Glands of an Invasive Whitefly
Su, Y., Li, J., Li, M., Luan, J., Ye, X.-D., Wang, X., & Liu, S. (2012) · PLoS ONE · doi:10.1371/journal.pone.0039303 · Cited by 109
“The raw reads cleaned by removing adaptor sequences, empty reads and low quality sequences (reads with unknown sequences ‘N’), were randomly clipped into 21 bp K-mers for assembly using de Bruijn graph and SOAPdenovo software [94].”
MethodPeng, Y., Lai, Z., Lane, T. S., Nageswara‐Rao, M., Okada, M., Jasieniuk, M., O’Geen, H., Kim, R. W., Sammons, R. D., Rieseberg, L. H., et al. (2014) · PLANT PHYSIOLOGY · doi:10.1104/pp.114.247668 · Cited by 106
“Using a modified strategy that has proven effective in vertebrates (Li et al., 2010a), date palm (Phoenix dactylifera; Al-Dous et al., 2011), and flax (Linum usitatissimum; Wang et al., 2012), the draft genome of horseweed was assembled into scaffolds.”
MethodJayaswall, K., Mahajan, P., Singh, G., Parmar, R., Seth, R., Raina, A. S., Swarnkar, M. K., Singh, A. K., Shankar, R., & Sharma, R. K. (2016) · Scientific Reports · doi:10.1038/srep30412 · Cited by 105
Niazi, A., Manzoor, S., Bejai, S., Meijer, J., & Bongcam‐Rudloff, E. (2014) · Standards in Genomic Sciences · doi:10.4056/sigs.4758653 · Cited by 106
Parizzi, L. P., Grassi, M. C. B., Calderón, L. A. L., Carazzolle, M. F., Queiroz, V. L., Lunardi, I., Zeidler, A. F., Teixeira, P. J. P. L., Mieczkowski, P. A., Rincones, J., et al. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-562 · Cited by 104
“The Illumina reads were submitted to the k-mer based correction tool of SOAPdenovo [76] and trimmed at various lengths prior to assembly.”
MethodMammalian Systems Biotechnology Reveals Global Cellular Adaptations in a Recombinant CHO Cell Line
Yusufi, F. N. K., Lakshmanan, M., Ho, Y. S., Loo, B. L. W., Ariyaratne, P. N., Yang, Y., Ng, S. K., Tan, T. R. M., Yeo, H. C., Lim, H. L., et al. (2017) · Cell Systems · doi:10.1016/j.cels.2017.04.009 · Cited by 105
Climate-driven flyway changes and memory-based long-distance migration
Gu, Z., Pan, S., Lin, Z., Li, H., Dai, X., Chang, J., Xue, Y., Su, H., Long, J., Sun, M., et al. (2021) · Nature · doi:10.1038/s41586-021-03265-0 · Cited by 105
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Krishnan, N. M., Pattnaik, S., Jain, P., Gaur, P., Choudhary, R., Vaidyanathan, S., Deepak, S., Hariharan, A. K., Krishna, P. B., Nair, J., et al. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-464 · Cited by 103
“5 kbp, 3 kbp and 10 kbp) mate-pair libraries, capillary Sanger sequencing reads generated from cloned neem genomic DNA and pyro-sequencing reads generated with IonTorrent Personal Genome Machine (Table S1 in Additional file 1) were used in assembling the neem genome with SOAPdenovo [16].”
MethodNeutral Genomic Microevolution of a Recently Emerged Pathogen, Salmonella enterica Serovar Agona
Zhou, Z., McCann, A., Litrup, E., Murphy, R. A., Cormican, M., Fanning, S., Brown, D., Guttman, D. S., Brisse, S., & Achtman, M. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003471 · Cited by 106
“Such genomic rearrangements might also account for the three other PFGE patterns with discrepant bands but we cannot exclude the possibility that these discrepancies represent rare local misassemblies with SOAPdenovo [59].”
InfluentialBiofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections
Soto-Girón, M. J., Rodriguez‐R, L. M., Luo, C., Elk, M., Ryu, H., Hoelle, J. M., Domingo, J. W. S., & Konstantinidis, K. T. (2016) · Applied and Environmental Microbiology · doi:10.1128/aem.03529-15 · Cited by 103
“(38), which combines Velvet (39), SOAPdenovo (40), and Newbler 2.”
BackgroundInfluentialCheng, X., Tian, X., Wang, Y., Lin, R.-M., Mao, Z., Chen, N., & Xie, B. (2013) · Scientific Reports · doi:10.1038/srep01869 · Cited by 103
Hahn, C., Fromm, B., & Bachmann, L. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu078 · Cited by 100
“…(20-mer) were subsequently calculated for this readpool using respective tools from the khmer package (Pell et al. 2012) in order to estimate the G. salaris genome size based on the k-mer frequency distribution (Li et al. 2010a) (see supplementary file S1, Section A, Supplementary Material online).”
MethodInfluentialMicrobial community adaptation to quaternary ammonium biocides as revealed by metagenomics
Oh, S., Tandukar, M., Pavlostathis, S. G., Chain, P., & Konstantinidis, K. T. (2013) · Environmental Microbiology · doi:10.1111/1462-2920.12154 · Cited by 102
“The hybrid protocol, which employs a combination of Velvet (Zerbino and Birney, 2008), SOAPdenovo (Li et al., 2010) and Newbler 2.”
MethodInfluentialMiyamoto, M., Motooka, D., Gotoh, K., Imai, T., Yoshitake, K., Goto, N., Iida, T., Yasunaga, T., Horii, T., Arakawa, K., et al. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-699 · Cited by 102
“To assemble massive amounts of short reads, a new type of algorithm using de Bruijn graphs has flourished, as illustrated by a series of genome assemblers including ABySS [5], ALLPATHS-LG [6], Velvet [7,8], and SOAPdenovo [9].”
InfluentialLi, X., Sun, H., Pei, J., Dong, Y., Wang, F., Chen, H., Sun, Y., Wang, N., Li, H., & Li, Y. (2012) · Gene · doi:10.1016/j.gene.2012.09.021 · Cited by 101
“All high-quality reads were assembled de novo by the SOAPdenovo program (Li et al., 2010), first into contigs using sequence overlap information until the contigs were no longer extended.”
MethodInfluentialSelf-citationSun, C., Fu, G., Zhang, C., Hu, J., Xu, L., Wang, R., Su, Y., Han, S., Yu, X., Cheng, H., et al. (2016) · Applied and Environmental Microbiology · doi:10.1128/aem.00204-16 · Cited by 101
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The genome of the miiuy croaker reveals well-developed innate immune and sensory systems
Xu, T., Xu, G., Che, R., Wang, R., Wang, Y., Li, J., Wang, S., Shu, C., Sun, Y., Liu, T., et al. (2016) · Scientific Reports · doi:10.1038/srep21902 · Cited by 101
Droplet barcoding for massively parallel single-molecule deep sequencing
Lan, F., Haliburton, J. R., Yuan, A., & Abate, A. R. (2016) · Nature Communications · doi:10.1038/ncomms11784 · Cited by 100
“continues on to pair with a reagent droplet generated on chip at (2) and the pair merges at the channel widening (3).”
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Self-citationSNP discovery by high-throughput sequencing in soybean
Wu, X., Ren, C., Joshi, T., Vuong, T. D., Xu, D. H., & Nguyen, H. T. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-469 · Cited by 104
“In addition, the short reads cannot be assembled to give complete sequence of complex plant genomes [21] and repeat sequences cannot be aligned unambiguously with the reference genome [22].”
BackgroundGenomics and Genetics of Human and Primate Y Chromosomes
Hughes, J. F., & Rozen, S. (2012) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090711-163855 · Cited by 100
“of the representation of all types of repeats, including segmental duplications, in the de novo WGS assemblies of two human individuals (76) exposed a dramatic artifactual loss of duplicated sequences (>99% missing) (2), confirming the intractability of Y ampliconic sequence to WGS approaches.”
BackgroundGeorges, A., Li, Q., Lian, J., O’Meally, D., Deakin, J. E., Wang, Z., Zhang, P., Fujita, M. K., Patel, H. R., Holleley, C. E., et al. (2015) · GigaScience · doi:10.1186/s13742-015-0085-2 · Cited by 101
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“Among the molecular function categories, nucleotide binding (46), other binding (103), other enzyme activity (54) and unknown molecular functions (44) were most abundant.”
BackgroundHu, J., Hao, Z.-Q., Frantz, L., Wu, S., Wu, C., Jiang, Y.-F., Wu, H., Kuang, W., Li, H., Zhang, Y., et al. (2020) · National Science Review · doi:10.1093/nsr/nwaa031 · Cited by 107
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“Finally, Trinity connects the contigs, and gets sequences that cannot be extended on either end.”
MethodInfluentialQiu, Z., Wan, L., Chen, T., Wan, Y., He, X., Lu, S., Wang, Y., & Lin, J. (2013) · New Phytologist · doi:10.1111/nph.12301 · Cited by 101
Kosugi, S., Hirakawa, H., & Tabata, S. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv465 · Cited by 101
Ku, C., Polychronakos, C., Tan, E., Naidoo, N., Yudi Pawitan, Y., Roukos, D. H., Mort, M. E., & Cooper, D. N. (2012) · Molecular Psychiatry · doi:10.1038/mp.2012.58 · Cited by 99
Bhardwaj, J., Chauhan, R., Swarnkar, M. K., Chahota, R. K., Singh, A. K., Shankar, R., & Yadav, S. K. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-647 · Cited by 98
“SOAPdenovo-trans was run for different k-mer lengths ranging from 19–71 bases.”
MethodInfluentialComplete Sequencing of Five Araliaceae Chloroplast Genomes and the Phylogenetic Implications
Li, R., Ma, P.-F., Wen, J., & Yi, T. (2013) · PLoS ONE · doi:10.1371/journal.pone.0078568 · Cited by 98
“First, we assembled raw sequence reads into contigs using SOAPdenovo [32] with an overlapping length of 31 bp.”
MethodSelf-citationGAM-NGS: genomic assemblies merger for next generation sequencing
Vicedomini, R., Vezzi, F., Scalabrin, S., Arvestad, L., & Policriti, A. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-s7-s6 · Cited by 99
“Even though some papers presented high quality assemblies based on NGS data (see [5,6]), de novo assembly, especially for large eukaryote genomes, is still a holy grail [7,8].”
BackgroundSynthetic long-read sequencing reveals intraspecies diversity in the human microbiome
Kuleshov, V., Jiang, C., Zhou, W., Jahanbani, F., Batzoglou, S., & Snyder, M. P. (2015) · Nature Biotechnology · doi:10.1038/nbt.3416 · Cited by 98
Wang, S.-S., Han, Y.-H., Ye, Y., Shi, X., Xiang, P., Chen, D., & Li, M. (2017) · RSC Advances · doi:10.1039/c7ra08391b · Cited by 100
Microbial phylogeny determines transcriptional response of resistome to dynamic composting processes
Wang, C., Dong, D., Strong, P. J., Zhu, W., Ma, Z., Qin, Y., & Wu, W. (2017) · Microbiome · doi:10.1186/s40168-017-0324-0 · Cited by 96
“High-quality short reads of the DNA sample were assembled by the SOAPdenovo assembler [29], as described in human gut microbiome metagenomic analyses [30].”
MethodGenomic Analyses Yield Markers for Identifying Agronomically Important Genes in Potato
Li, Y., Colleoni, C., Zhang, J., Liang, Q., Hu, Y., Ruess, H., Simon, R., Liu, Y., Liu, H., Yu, G., et al. (2018) · Molecular Plant · doi:10.1016/j.molp.2018.01.009 · Cited by 97
Self-citationCristino, A. S., Tanaka, É. D., Rubio, M., Piulachs, M., & Bellés, X. (2011) · PLoS ONE · doi:10.1371/journal.pone.0019350 · Cited by 98
“(EPS) Figure S3 Pipeline used for assembling the sequences using Velvet, SOAPdenovo and phrap softwares.”
MethodHigh throughput DNA sequencing: The new sequencing revolution
Delseny, M., Han, B., & Hsing, Y. I. (2010) · Plant Science · doi:10.1016/j.plantsci.2010.07.019 · Cited by 102
Omega: an Overlap-graphde novoAssembler for Metagenomics
Haider, B., Ahn, T.-H., Bushnell, B., Chai, J., Copeland, A., & Pan, C. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu395 · Cited by 96
CNV discovery for milk composition traits in dairy cattle using whole genome resequencing
Gao, Y., Jiang, J., Yang, S., Hou, Y., Liu, G. E., Zhang, S., Zhang, Q., & Sun, D. (2017) · BMC Genomics · doi:10.1186/s12864-017-3636-3 · Cited by 96
“Sequence assembly (AS) method [62, 63] could discover all kinds of genetic variations theoretically because of its fine-scale working.”
MethodIncipient diploidization of the medicinal plant Perilla within 10,000 years
Zhang, Y.-J., Shen, Q., Leng, L., Zhang, D., Chen, S., Shi, Y., Ning, Z., & Chen, S.-L. (2021) · Nature Communications · doi:10.1038/s41467-021-25681-6 · Cited by 85
Transcriptome and proteomic analysis of mango (Mangifera indica Linn) fruits
Wu, H., Jia, H., Ma, X., Wang, S., Yao, Q., Xu, W., Zhou, Y.-G., Gao, Z., & Zhan, R. (2014) · Journal of Proteomics · doi:10.1016/j.jprot.2014.03.030 · Cited by 96
“Transcriptome short reads were obtained using the SOAPdenovo assembly program [33] with the following parameters: min_contig_length = 100, min_glue = 2, group_pairs_distance = 250, path_reinforcement_distance = 85, min_kmer_cov = 2, k = 25 by BGI and the short-read assembly program Trinity [34].”
MethodHuang, J., Zhao, Y., Shiraigol, W., Li, B., Bai, D., Ye, W., Daidiikhuu, D., Yang, L., Jin, B., Zhao, Q., et al. (2014) · Scientific Reports · doi:10.1038/srep04958 · Cited by 100
Deep Insight into the Ganoderma lucidum by Comprehensive Analysis of Its Transcriptome
Yu, G., Wang, M., Huang, J. S., Yin, Y.-L., Chen, Y., Jiang, S., Jin, Y., Lan, X., Wong, B. H. C., Liang, Y. W., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0044031 · Cited by 96
“cn) which implements a de Bruijn graph algorithm [80].”
MethodXu, Y., Zhou, W., Zhou, Y., Wu, J., & Zhou, X. (2012) · PLoS ONE · doi:10.1371/journal.pone.0036238 · Cited by 95
“After removal of low quality reads, processed reads were assembled using Short Oligonucleotide Analysis Package (SOAP) de novo software and clustered with TIGR Gene Indices (TGI) Clustering tools [64].”
MethodXu, Y., Minhazul, K. A. H. M., Wang, X., Liu, X., Li, X., Meng, Q., Li, H., Zhang, C., Sun, X., & Sun, B. (2020) · Environmental Pollution · doi:10.1016/j.envpol.2020.114506 · Cited by 95
Li, J., Zhong, H., Ramayo‐Caldas, Y., Terrapon, N., Lombard, V., Potocki-Véronèse, G., Estellé, J., Popova, M., Yang, Z., Zhang, H., et al. (2020) · GigaScience · doi:10.1093/gigascience/giaa057 · Cited by 101
“06 [47], -”
Self-citationDesai, A., Marwah, V. S., Yadav, A. R., Jha, V., Dhaygude, K., Bangar, U., Kulkarni, V., & Jere, A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0060204 · Cited by 100
“05, 14-02-2011) [27], Velvet [28], Meraculous [29] IDBA-UD [30] and ABySS [31] were selected for this study.”
BackgroundMethodInfluentialNaim, F., Nakasugi, K., Crowhurst, R. N., Hilario, E., Zwart, A. B., Hellens, R. P., Taylor, J. M., Waterhouse, P. M., & Wood, C. C. (2012) · PLoS ONE · doi:10.1371/journal.pone.0052717 · Cited by 94
“05) [32] with a hash length of 65 and minimum scaffold length of 201 bases.”
BackgroundHe, L., Wang, Q., Jin, X., Wang, Y., Chen, L., Liu, L., & Wang, Y. (2012) · PLoS ONE · doi:10.1371/journal.pone.0033735 · Cited by 94
“Assembly Transcriptome de novo assembly was carried out with the short read assembling program SOAPdenovo [16].”
MethodSequencing consolidates molecular markers with plant breeding practice
Yang, H., Li, C., Lam, H., Clements, J. C., Yan, G., & Zhao, S. (2015) · Theoretical and Applied Genetics · doi:10.1007/s00122-015-2499-8 · Cited by 96
“One exception is MFLP markers, where DNA polymorphisms can be easily converted into cost-effective and sequencespecific PCR markers (Yang et al. 2002, 2004, 2008, 2010; Boersma et al. 2007a, b, 2009; Li et al. 2010b, 2011, 2012a, 1 3 b).”
BackgroundMethodInfluentialSelf-citationTranscriptomic analysis of rice (Oryza sativa) endosperm using the RNA-Seq technique
Gao, Y., Xu, H., Shen, Y., & Wang, J. (2013) · Plant Molecular Biology · doi:10.1007/s11103-013-0009-4 · Cited by 94
“Transcriptome de novo assembly was aligned to the rice genome assembling program SOAPdenovo (http://www.soap.genomics.org.cn/soapdenovo.html) (Li et al. 2009) A digital gene was performed on the uniquely mapped to the genome if it includes reads mapped to the reference genomes with no more than two…”
Self-citationTan, Z., Yang, T., Wang, Y., Xing, K., Zhang, F., Zhao, X., Ao, H., Chen, S., Liu, J., & Wang, C. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01546 · Cited by 94
“Using SOAPdenovo software (version 1.05), which is based on the De-Bruijn graph (Li et al., 2010), the filtered data were assembled by different sizes of Kmer (51, 55, 59, and 63).”
MethodInfluentialXie, M., Wu, J., An, F., Yue, X., Tao, D., Wu, R., & Lee, Y. K. (2018) · Food Research International · doi:10.1016/j.foodres.2018.10.076 · Cited by 94
Microbial synergistic interactions for reductive dechlorination of polychlorinated biphenyls
Wang, S., Chen, C., Zhao, S., & He, J. (2019) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2019.02.283 · Cited by 94
Tan, L., Wang, L., Wei, K., Zhang, C., Wu, L., Qi, G.-N., Cheng, H., Zhang, Q., Cui, Q., & Liang, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0081611 · Cited by 93
Hao, D., Ma, P., Mu, J., Chen, S., Xiao, P., Peng, Y. L., Huo, L., Xu, L., & Sun, C. (2012) · Science China Life Sciences · doi:10.1007/s11427-012-4319-6 · Cited by 93
The Genome of the Trinidadian Guppy, Poecilia reticulata, and Variation in the Guanapo Population
Künstner, A., Hoffmann, M., Fraser, B. A., Kottler, V. A., Sharma, E., Weigel, D., & Dreyer, C. (2016) · PLoS ONE · doi:10.1371/journal.pone.0169087 · Cited by 91
“05 [40] (kmer size 27, -d 1, -D 2, -F) was used.”
Luo, J., Chai, J., Wen, Y., Tao, M., Lin, G., Liu, X., Li, R., Chen, Z., Wu, S., Li, S., et al. (2020) · Science Advances · doi:10.1126/sciadv.aaz7677 · Cited by 95
Self-citationOn the Representation of de Bruijn Graphs
Chikhi, R., Limasset, A., Jackman, S. D., Simpson, J. T., & Medvedev, P. (2014) · Lecture notes in computer science · doi:10.1007/978-3-319-05269-4_4 · Cited by 92
Huang, H., Xu, L., Tong, Z., Lin, E.-P., Liu, Q., Cheng, L., & Zhu, M. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-648 · Cited by 93
“html) with the default settings, except for the k-mer value, which was set at a specific chosen value [32].”
BackgroundMethodBioinformatics for the Human Microbiome Project
Gevers, D., Pop, M., Schloss, P. D., & Huttenhower, C. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002779 · Cited by 91
“Informed by these results, however, we proceeded to develop an assembly strategy around the SOAPdenovo assembler as used in the MetaHIT project in order to simplify comparisons to data generated in this earlier study.”
MethodInfluentialYoung, N. D., Jex, A. R., Cantacessi, C., Hall, R. S., Campbell, B. E., Spithill, T. W., Tangkawattana, S., Tangkawattana, P., Laha, T., & Gasser, R. B. (2011) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0001004 · Cited by 91
“04 [42].”
Indriolo, E., Tharmapalan, P., Wright, S., & Goring, D. R. (2012) · The Plant Cell · doi:10.1105/tpc.112.104943 · Cited by 91
Pootakham, W., Sonthirod, C., Naktang, C., Ruang‐areerate, P., Yoocha, T., Sangsrakru, D., Theerawattanasuk, K., Rattanawong, R., Lekawipat, N., & Tangphatsornruang, S. (2017) · Scientific Reports · doi:10.1038/srep41457 · Cited by 92
Current challenges and solutions of de novo assembly
Liao, X., Li, M., Zou, Y. F., Wu, F., Yi‐Pan, & Wang, J. (2019) · Quantitative Biology · doi:10.1007/s40484-019-0166-9 · Cited by 90
“Typical k-mer counting-based error 98 © Higher Education Press and Springer-Verlag GmbH Germany, part of Springer Nature 2019 correction methods includes: Bless [77], Quack [79], Reptile [80], SOAPec2 [81], EDAR [82].”
MethodSelf-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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