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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
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Characterization of the Lycium barbarum fruit transcriptome and development of EST-SSR markers
Chen, C., Xu, M., Wang, C., Qiao, G., Wang, W., Tan, Z., Wu, T., & Zhang, Z. (2017) · PLoS ONE · doi:10.1371/journal.pone.0187738 · Cited by 45
Li, Y., Li, Y., Jin, W., Sharpton, T. J., Mackie, R. I., Cann, I., Cheng, Y., & Zhu, W. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00435 · Cited by 46
Self-citationUllah, M., Raza, A., Li, Y., & Yu, Z. (2019) · Microorganisms · doi:10.3390/microorganisms7070188 · Cited by 45
“The bioinformatics assembly tools used in the in-house-developed pipeline include COPE [18], SOAPdenovo [19], and Newbler [20].”
MethodSelf-citationEvaluation of the Effects of Different Bacteroides vulgatus Strains against DSS-Induced Colitis
Li, S., Wang, C., Zhang, C., Luo, Y., Cheng, Q., Yu, L., & Sun, Z. (2021) · Journal of Immunology Research · doi:10.1155/2021/9117805 · Cited by 45
“vulgatus strains was performed using the Illumina HiSeq System by Majorbio (China), as described in a previous study [36, 37].”
MethodSelf-citationZhao, J., Li, B. J., Lv, P., Hou, J., Qiu, Y., & Huang, X. (2021) · Frontiers of Environmental Science & Engineering · doi:10.1007/s11783-021-1469-4 · Cited by 45
“After quality control, the clean reads were assembled into contigs employing SOAPdenovo assembler (Li et al., 2010).”
MethodQin, X., Zhang, J., Liu, Y., Guo, Y., Tang, Y. X., Zhang, Q., Ma, Q., Ji, C., & Zhao, L. (2022) · Food Control · doi:10.1016/j.foodcont.2022.108834 · Cited by 44
Sander, A. F., Lavstsen, T., Rask, T. S., Lisby, M., Salanti, A., Fordyce, S. L., Jespersen, J. S., Carter, R., Deitsch, K., Theander, T. G., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1174 · Cited by 46
“Paired-end reads from each progeny were de novo assembled separately using SOAPdenovo (32) (settings: k-mer size of 57 bp andmedian insert size as determined from the mapping) and compared with parental genes by alignment.”
MethodHuang, D., Zhang, Y., Jin, M., Li, H., Song, Z., Wang, Y., & Chen, J. (2013) · Molecular Ecology Resources · doi:10.1111/1755-0998.12197 · Cited by 44
“The paired-end Illumina reads were assembled using SOAPdenovo (Li et al. 2010).”
MethodAn, F., Zou, Z., Cai, X., Wang, J., Rookes, J. E., Weifu, L., Cahill, D. M., & Kong, L. (2015) · PLoS ONE · doi:10.1371/journal.pone.0125595 · Cited by 44
“Gene annotation and alignments indicated that 10 unigenes were putative aquaporin encoding sequences (see S1 File) in the 54495 unigenes longer than 200 bp obtained by SOAP de novo assembly [38].”
Self-citationA Proteomic Survey of Nonribosomal Peptide and Polyketide Biosynthesis in Actinobacteria
Chen, Y., Ntai, I., Ju, K., Unger, M., Zamdborg, L., Robinson, S. J., Doroghazi, J. R., Labeda, D. P., Metcalf, W. W., & Kelleher, N. L. (2011) · Journal of Proteome Research · doi:10.1021/pr2009115 · Cited by 44
Yang, H., Jian, J., Li, X., Renshaw, D., Clements, J. C., Sweetingham, M. W., Tan, C., & Li, C. (2015) · BMC Genomics · doi:10.1186/s12864-015-1878-5 · Cited by 44
“The sequence reads for each cultivar were assembled into scaffolds using the software program SOAPdenovo [45], and the N50 of assembled scaffolds for each cultivar ranged from 7,633 bp to 10,864 bp (Table 1).”
MethodInfluentialSelf-citationLi, B., & Kimmel, M. (2013) · Genetics · doi:10.1534/genetics.113.154161 · Cited by 44
Luo, Y., Ma, P., Li, H., Yang, J., Wang, H., & Li, D.-Z. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evv260 · Cited by 44
Duan, X., Wang, K., Su, S., Tian, R., Li, Y., & Chen, M. (2017) · PLoS ONE · doi:10.1371/journal.pone.0172513 · Cited by 45
Self-citationChen, N. W. G., Serres-Giardi, L., Ruh, M., Briand, M., Bonneau, S., Darrasse, A., Barbe, V., Gagnevin, L., Koebnik, R., & Jacques, M. (2018) · BMC Genomics · doi:10.1186/s12864-018-4975-4 · Cited by 44
Liu, W., Chen, L., Cai, Y., Zhang, Q., & Bian, Y. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19092525 · Cited by 44
“12) was used to fill gaps in the assembly with the Illumina paired-end data [65], followed by the use the finisherSC software to connect the scaffolds and fill the gaps with the PacBio data [66].”
MethodWong, K., Zhang, J., Yan, S., Li, X., Lin, Q., Kwong, S., & Liang, C. (2019) · ACM Computing Surveys · doi:10.1145/3340286 · Cited by 50
“SOAP [85] and ALLPATHS-LG [40] are recommended for large and repeat-rich vertebrate genomes (e.g., human and mouse).”
BackgroundWang, C., Li, S., Hong, K., Yu, L., Tian, F., Zhao, J., Zhang, H., Chen, W., & Zhai, Q. (2021) · Food & Function · doi:10.1039/d1fo00875g · Cited by 41
Self-citationYang, P., Zhu, J., Gong, Z., Xu, D.-L., Chen, X.-M., Liu, W., Lin, X.-D., & Li, Y. (2012) · PLoS ONE · doi:10.1371/journal.pone.0035719 · Cited by 44
“After filtering dirty raw reads, de novo assembly of transcriptome was carried out using a short read assembly program called SOAP [27].”
MethodSelf-citationWang, L., Liu, Q., Chen, Y., Zheng, X., Wang, C., Qi, Y., Dong, Y., Xiao, Y., Chen, C., Chen, T., et al. (2022) · Microbiome · doi:10.1186/s40168-022-01278-z · Cited by 43
Self-citationIdentifying SNPs without a Reference Genome by Comparing Raw Reads
Peterlongo, P., Schnel, N., Pisanti, N., Sagot, M., & Lacroix, V. (2010) · Lecture notes in computer science · doi:10.1007/978-3-642-16321-0_14 · Cited by 43
“A category of de novo read-assembly methods such as SOAPdenovo [7], Euler [8] and Velvet [11] (to mention a few) uses the de Bruijn graph as a fundamental data structure.”
MethodPopIns: population-scale detection of novel sequence insertions
Kehr, B., Melsted, P., & Halldórsson, B. V. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv273 · Cited by 43
“Contact: birte.kehr@decode.is Supplementary information: Supplementary data are available at Bioinformatics online.”
BackgroundYao, B., Zhao, Y., Zhang, H., Zhang, M., Liu, M., Liu, H., & Li, J. (2012) · Biotechnology Letters · doi:10.1007/s10529-011-0841-z · Cited by 42
“The reads obtained were randomly clipped into different K-mers for assembly using de Bruijn graph and SOAPdenovo software (Li et al. 2010).”
InfluentialMapsembler, targeted and micro assembly of large NGS datasets on a desktop computer
Peterlongo, P., & Chikhi, R. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-48 · Cited by 43
“5% of the contigs from a SOAPdenovo [12] wholegenome assembly of the same dataset align perfectly to the reference.”
BackgroundInfluentialTranscriptome sequencing of rhizome tissue of Sinopodophyllum hexandrum at two temperatures
Kumari, A., Singh, H. R., Jha, A., Swarnkar, M. K., Shankar, R., & Kumar, S. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-871 · Cited by 43
“De novo assembling of high quality reads was performed using SOAPdenovo tool [21].”
MethodMolnar, M., & Ilie, L. (2014) · Briefings in Bioinformatics · doi:10.1093/bib/bbu029 · Cited by 43
“Therefore, a large number of error-correcting programs have been designed, including Euler [6], SHREC [7], Recount [8], Reptile [9], Quake [10], CUDA [11], HSHREC [12], SOAP [13], HiTEC [14], Coral [15], DecGPU [16], Hammer [17], ECHO [18], PSAEC [19], MyHybrid [20], SGA [21], RACER [22], Musket [23] and BLESS [24]; s…”
MethodMousavi, M., Tong, C., Liu, F., Tao, S., Wu, J., Li, H., & Shi, J. (2016) · BMC Genomics · doi:10.1186/s12864-016-3003-9 · Cited by 43
“Each parental genome was then assembled from its corrected short reads using SOAPdenovo [40], which builds contigs using a de Bruijn graph algorithm.”
MethodInfluentialJiang, L., Xiao, J., Liu, L., Pan, Y., Yan, S., & Wang, Y. (2017) · VirusDisease · doi:10.1007/s13337-017-0394-4 · Cited by 43
“The prediction and annotation of open reading frames (ORFs) in WSSV-CN-Pc were conducted according to the procedures described previously [13].”
MethodGenome survey and SSR analysis of Apocynum venetum
Li, G., Song, L.-X., Jin, C.-Q., Li, M., Gong, S.-P., & Wang, Y. (2019) · Bioscience Reports · doi:10.1042/bsr20190146 · Cited by 43
Wang, L., Ma, G., Wang, H., Cheng, C., Mu, S., Quan, W., Jiang, L., Zhao, Z., Zhang, Y., Zhang, K., et al. (2019) · GigaScience · doi:10.1093/gigascience/giz116 · Cited by 43
“141 Genome assembly 142 The primary assembled genome was generated by SOAPdenovo [43] (version 2.”
InfluentialTherapeutic effect of the YH6 phage in a murine hemorrhagic pneumonia model
Yang, M., Du, C., Gong, P., Xia, F., Sun, C., Feng, X., Lei, L., Song, J. I., Zhang, L., Wang, B., et al. (2015) · Research in Microbiology · doi:10.1016/j.resmic.2015.07.008 · Cited by 43
Li, H.-W., Zhi, X., Yao, J.-C., Zhou, Y. G., Tang, S., Klenk, H., Zhao, J., & Li, W. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061528 · Cited by 43
“The paired-end reads were assembled using SOAPdenovo [58].”
MethodMSPKmerCounter: A Fast and Memory Efficient Approach for K-mer CountingPreprint
Li, Y., & XifengYan (2015) · arXiv (Cornell University) · doi:10.48550/arxiv.1505.06550 · Cited by 65
“For the short read sequences generated from mammalian-sized genomes, software like Euler, Velvet, AllPaths and SOAPdenovo will not be able to finish assembling successfully within a reasonable amount of memory.”
BackgroundMethodInfluentialSelf-citationWu, Y., Xia, M., Zhang, X., Li, X., Zhang, R., Yan, Y., Lang, F., Zheng, Y., & Wang, M. (2021) · Food Science & Nutrition · doi:10.1002/fsn3.2409 · Cited by 42
Pasipoularides, A. D. (2015) · Journal of Cardiovascular Translational Research · doi:10.1007/s12265-015-9630-8 · Cited by 41
Assembler for de novo assembly of large genomes
Chu, T.-C., Lu, C.-H., Liu, T., Lee, G. C., Li, W., & Shih, A. C.-C. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1314090110 · Cited by 42
“For ALLPATHS-LG and SOAPdenovo, the time recorded was the run time rather than the CPU time.”
BackgroundMethodInfluentialOnishi‐Seebacher, M., & Korbel, J. O. (2011) · BioEssays · doi:10.1002/bies.201100075 · Cited by 43
Wang, S., Chng, K. R., Chen, C., Bedard, D. L., & He, J. (2015) · Environmental Science & Technology · doi:10.1021/acs.est.5b01979 · Cited by 42
Molecular subtyping and erythromycin resistance ofCampylobacterin China
Zhang, A., Song, L., Liang, H., Gu, Y., Zhang, C., Liu, X., Zhang, J., & Zhang, M. (2016) · Journal of Applied Microbiology · doi:10.1111/jam.13135 · Cited by 42
“Short reads were assembled into genome sequences using SOAPDENOVO 2.04 (Li et al. 2010).”
MethodInfluentialGao, B., Jin, M., Li, L., Qu, W., & Zeng, R. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00600 · Cited by 42
Ma, P., Vorontsova, M. S., Nanjarisoa, O. P., Razanatsoa, J., Guo, Z., Haevermans, T., & Li, D.-Z. (2017) · BMC Plant Biology · doi:10.1186/s12870-017-1199-8 · Cited by 42
Repeat-Preserving Decoy Database for False Discovery Rate Estimation in Peptide Identification
Moosa, J. M., Guan, S., Moran, M. F., & Ma, B. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.9b00555 · Cited by 42
Lijing, P., Chen, J., Ren, S., Shen, H., Rong, B., Liu, W., & Yang, Z. (2020) · Archives of Microbiology · doi:10.1007/s00203-020-01924-w · Cited by 42
Tsai, K. J., Lu, M. J., Yang, K.-J., Li, M., Teng, Y.-C., Chen, S., Ku, M. S. B., & Li, W. (2016) · Scientific Reports · doi:10.1038/srep35076 · Cited by 41
Itakura, S., Yoshikawa, Y., Togami, Y., & Umezawa, K. (2020) · Journal of Asia-Pacific Entomology · doi:10.1016/j.aspen.2020.05.004 · Cited by 41
Gonzalez-Beltran, A. N., Li, P., Zhao, J., Ávila-García, M. S., Roos, M., Thompson, M., van der Horst, E., Kaliyaperumal, R., Luo, R., Lee, T., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0127612 · Cited by 45
“Improvements were made at each step of the de Bruijn graph based algorithm implemented by SOAPdenovo1.”
ResultInfluentialDeciphering the human microbiome using next-generation sequencing data and bioinformatics approaches
Kim, Y., Koh, I., & Rho, M. (2014) · Methods · doi:10.1016/j.ymeth.2014.10.022 · Cited by 44
Optimization of De Novo Short Read Assembly of Seabuckthorn (Hippophae rhamnoides L.) Transcriptome
Ghangal, R., Chaudhary, S., Jain, M., Purty, R. S., & Sharma, P. C. (2013) · PLoS ONE · doi:10.1371/journal.pone.0072516 · Cited by 42
“24 million) were assembled separately using Velvet, Oases, ABySS and SOAPdenovo programs at different k-mer lengths ranging from 21 to 81, whereas CLC Genomics Workbench and Trinity were used at default parameters (Table S1).”
MethodInfluentialYang, D., Fu, Y., Wu, X., Xie, Y., Nie, H., Chen, L., Nong, X., Gu, X., Wang, S., Peng, X., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0032283 · Cited by 39
“html) [49].”
SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores
Meng, J., Wang, B., Wei, Y., Feng, S., & Balaji, P. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-s9-s2 · Cited by 41
“By comparing with several state-of-the-art sequential and parallel assemblers, such as Velvet [22], SOAPdenovo [29], Pasha [16], ABySS [14] and Ray [15], we evaluate the scalability, quality of contigs in terms of N50, error rate and coverage for SWAP-Assembler.”
MethodOlive fly transcriptomics analysis implicates energy metabolism genes in spinosad resistance
Sagri, E., Reczko, M., Gregoriou, M., Tsoumani, K. T., Zygouridis, N. E., Salpea, K. D., Zalom, F. G., Ragoussis, J., & Mathiopoulos, K. D. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-714 · Cited by 41
“The reads of the libraries were assembled to construct the reference transcriptome using the SOAPdenovo assembler [39] with a word size of 25 nt and using all paired and unpaired reads.”
MethodCombinatorial Pooling Enables Selective Sequencing of the Barley Gene Space
Lonardi, S., Duma, D., Alpert, M., Cordero, F., Beccuti, M., Bhat, P. R., Wu, Y., Ciardo, G., Alsaihati, B. A., Ma, Y., et al. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003010 · Cited by 41
“the table we had to use SOAPDENOVO [25], however VELVET and”
InfluentialMisassembly detection using paired-end sequence reads and optical mapping data
Muggli, M. D., Puglisi, S. J., Ronen, R., & Boucher, C. A. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv262 · Cited by 41
“Availability and implementation: MISSEQUEL can be used as a post-processing step in combination with any genome assembler and is freely available at http://www.cs.colostate.edu/seq/.”
BackgroundMethodYang, E., Chow, F. W., Wang, G., Woo, P. C. Y., Lau, S. K. P., Yuen, K., Lin, X., & Cai, J. J. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004662 · Cited by 41
“Phrap was used to assemble Sanger reads, while ABySS [17] and SOAPdenovo [18] were used to assemble Illumina reads.”
MethodVarga, J. J., Barbier, M., Mulet, X., Bielecki, P., Bartell, J. A., Owings, J. P., Martínez-Ramos, I., Hittle, L. E., Davis, M. R., Damron, F. H., et al. (2015) · BMC Genomics · doi:10.1186/s12864-015-2069-0 · Cited by 41
“de novo assembly was accomplished using SOAP DeNovo [154].”
MethodAraki, K., Aokic, J.-Y., Kawase, J., Hamada, K., Ozaki, A., Fujimoto, H., Yamamoto, I., & Usuki, H. (2018) · International Journal of Genomics · doi:10.1155/2018/7984292 · Cited by 40
Transposon proliferation in an asexual parasitoid
Kraaijeveld, K., ZWANENBURG, B., HUBERT, B., Vieira, C. P., de Pater, S., van Alphen, J. J. M., den Dunnen, J. T., & de Knijff, P. (2012) · Molecular Ecology · doi:10.1111/j.1365-294x.2012.5582.x · Cited by 41
“age, and each was assembled de novo using SOAPdenovo (Li et al. 2010) (k-mer = 31).”
MethodHoang, N. V., Sogbohossou, D. E. O., Xiong, W., Simpson, C. J. C., Singh, P., Walden, N., van den Bergh, E., Becker, F. F. M., Li, Z., Zhu, X., et al. (2023) · The Plant Cell · doi:10.1093/plcell/koad018 · Cited by 40
“21 (Li et al., 2010), with a k-mer of 63.”
Purdy, K. J., Hurd, P. J., Moya‐Laraño, J., Trimmer, M., Oakley, B. B., & Woodward, G. (2010) · Advances in ecological research/Advances in Ecological Research · doi:10.1016/b978-0-12-385005-8.00003-4 · Cited by 42
Hand, M. L., SPANGENBERG, G. C., Forster, J. W., & Cogan, N. O. I. (2013) · G3 Genes Genomes Genetics · doi:10.1534/g3.112.005264 · Cited by 40
Chang, Y.-J., Chen, C.-C., Chen, C.-L., & Ho, J.-M. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-s7-s28 · Cited by 40
“It is noteworthy that some assemblers e.g., Bambus2 [22] [8], have lower precision and recall due to the fact that their misjoined errors and longer indels occur in longer contigs.”
BackgroundThe complete genome of a viable archaeum isolated from 123‐million‐year‐old rock salt
Jaakkola, S., Pfeiffer, F., Ravantti, J., Guo, Q., Liu, Y., Chen, X., Ma, H., Yang, C., Oksanen, H. M., & Bamford, D. H. (2015) · Environmental Microbiology · doi:10.1111/1462-2920.13130 · Cited by 40
Intelligent mining of large-scale bio-data: Bioinformatics applications
Hashemi, F. S. G., Ismail, M. R., Rafii, M. Y., Hashemi, M. S. G., Nadimi-Shahraki, M. H., Rastegari, H., Miah, G., & Aslani, F. (2017) · Biotechnology & Biotechnological Equipment · doi:10.1080/13102818.2017.1364977 · Cited by 44
“The Maq algorithm utilizes hashing methods [69].”
Bioconversion of lignin into bioplastics by Pandoraea sp. B-6: molecular mechanism
Liu, D., Xu, Y., Si, M., Deng, X., Min, X., Shi, Y., & Chai, L. (2018) · Environmental Science and Pollution Research · doi:10.1007/s11356-018-3785-1 · Cited by 39
Ji, Y., Cheng, M., Zhai, S., Xi, H., Cai, R., Wang, Z., Zhang, H., Wang, X., Xue, Y., Li, X., et al. (2018) · Veterinary Microbiology · doi:10.1016/j.vetmic.2018.12.021 · Cited by 40
Yi, X., Gao, Q., Zhang, L., Wang, X., He, Y., Hu, F., Zhang, J., Zou, G., Yang, S., Zhou, Z., et al. (2019) · Biotechnology for Biofuels · doi:10.1186/s13068-019-1466-z · Cited by 40
Liu, W. J., Li, J., Zou, R., Pan, J., Jin, T., Li, L., Liu, P., Zhao, Y., Yu, X., Wang, H., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2013267117 · Cited by 40
An Introduction to Whole-Metagenome Shotgun Sequencing Studies
Joseph, T., & Pe’er, I. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1103-6_6 · Cited by 43
Chen, B., Gui, F., Xie, B., Deng, Y., Sun, X., Lin, M., Tao, Y., & Li, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0058780 · Cited by 40
“Three libraries of DNA fragments with insert sizes of 500 bp, 2000 bp and 5000 bp were generated and all of the reads produced from the three libraries were assembled using the SOAPdenovo [15] assembler (http:// soap.”
MethodSelf-citationChen, P., Ran, S., Li, R., Huang, Z., Qian, J., Yu, M., & Zhou, R. (2014) · Molecular Breeding · doi:10.1007/s11032-014-0146-8 · Cited by 39
“Transcriptome de novo assembly was carried out with a short read assembly program—SOAPdenovo (Li et al. 2010).”
MethodSelf-citationShih, M., Chou, M., Yue, J.-J., Hsu, C.-T., Chang, W., Ko, S., Liao, D., Huang, Y., Chen, J. J. W., Yuan, J.-L., et al. (2014) · BMC Plant Biology · doi:10.1186/1471-2229-14-179 · Cited by 39
“Recently, it was reported that OsMADS6/MOSAIC FLORAL ORGANS 1 (MFO1) plays a synergistic role in regulating floral organ identity, floral meristem determinacy and meristem fate with class B (OsMADS16), C (OsMADS3), and D (OsMADS13) genes and with the YABBY gene DROOPING LEAF (DL), which was previously known to functio…”
BackgroundImproving mammalian genome scaffolding using large insert mate-pair next-generation sequencing
van Heesch, S., Kloosterman, W. P., Lansu, N. R., Ruzius, F.-P., Levandowsky, E., Lee, C. C., Zhou, S., Goldstein, S., Schwartz, D. C., Harkins, T. T., et al. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-257 · Cited by 40
“Furthermore, most ongoing genome sequencing projects employ next-generation sequencing techniques, and because de novo genome assembly based on short-reads is still in its infancy, contig sizes for vertebrate genomes are typically in the kilobase range [19,28,29].”
BackgroundDing, C., Rogers, M. J., Yang, K., & He, J. (2017) · Environmental Microbiology · doi:10.1111/1462-2920.13817 · Cited by 40
“Genomes were assembled by using SOAPdenovo package with optimized parameters (Li et al., 2010).”
MethodTakamatsu, T., Baslam, M., Inomata, T., Oikawa, K., Itoh, K., Ohnishi, T., Kinoshita, T., & Mitsui, T. (2018) · Frontiers in Plant Science · doi:10.3389/fpls.2018.00266 · Cited by 39
Sun, J. Y., Qian, S., Lu, J. N., Liu, Y., Lü, F., Bie, X., & Lu, Z. (2018) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.8b00418 · Cited by 39
Xu, L., Chen, Y.-T., Wang, Z., Zhang, Y., He, Y., Zhang, A., Chen, H., & Xue, G. (2022) · Chemosphere · doi:10.1016/j.chemosphere.2022.137256 · Cited by 39
Mao, Z., Li, M., & Chen, J. (2013) · Genome Announcements · doi:10.1128/genomea.00586-13 · Cited by 39
“Genome sequences were assembled by SOAPdenovo (7), resulting in 87 contigs ( 500 bp in size) with an N50 length of 159,696 bp, and a total length of about 5.4 Mb.”
MethodInfluentialComparison of the Transcriptome between Two Cotton Lines of Different Fiber Color and Quality
Gong, W., He, S., Tian, J., Sun, J., Pan, Z., Jia, Y., Sun, G., & Du, X. (2014) · PLoS ONE · doi:10.1371/journal.pone.0112966 · Cited by 39
“The clean reads de novo assembly was carried out using the short reads assembling program-SOAPdenovo [18].”
MethodPerpendicular axes of differentiation generated by mitochondrial introgression
Morales, H. E., Sunnucks, P., Joseph, L., & Pavlova, A. (2017) · Molecular Ecology · doi:10.1111/mec.14114 · Cited by 40
“05 with a K-mer size of 35 and default settings (Li et al. 2010).”
BackgroundMethodInfluentialHong, H., Zhang, W., Shen, J., Su, Z., Ning, B., Han, T., Perkins, R., Shi, L. M., & Tong, W. (2013) · Science China Life Sciences · doi:10.1007/s11427-013-4439-7 · Cited by 40
Scholz, M. B., Lo, C., & Chain, P. (2014) · Scientific Reports · doi:10.1038/srep06480 · Cited by 38
“Forthepurposesofthispaper,SOAPdenovo 16 , as well as CLC Bio de novo assembler and Velvet 7 , were used for all individual Illumina assemblies, with a range of Kmers, typically from 21–31, for the data described here, and using the ranges from 45–105 for samples with longer Illumina reads.”
MethodBasal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing
Chen, M., Zou, M., Yang, L., & He, S. (2012) · PLoS ONE · doi:10.1371/journal.pone.0036256 · Cited by 38
“Short reads were assembled to construct contigs using SOAPdenovo software [36].”
MethodWhole-Genome Sequence of a Multidrug-Resistant Clinical Isolate of Acinetobacter lwoffii
Hu, Y., Zhang, W., Liang, H., Liu, L., Peng, G., Pan, Y., Yang, X., Zheng, B., Gao, G. F., Zhu, B., et al. (2011) · Journal of Bacteriology · doi:10.1128/jb.05617-11 · Cited by 38
“paired-end reads were assembled by SOAPdenovo (5), and a final assembly with only one scaffold was obtained.”
MethodDe novo assembly of the transcriptome of an invasive snail and its multiple ecological applications
Sun, J., Wang, M., Wang, H., Zhang, H., Zhang, X., Thiyagarajan, V., Qian, P., & Qiu, J. (2012) · Molecular Ecology Resources · doi:10.1111/1755-0998.12014 · Cited by 38
“SOAPdenovo version 1.04 was used for transcriptome assembly (Li et al. 2009).”
BackgroundMethodInfluentialFraley, S. I., Athamanolap, P., Masek, B. J., Hardick, J. P., Carroll, K. C., Hsieh, Y., Rothman, R. E., Gaydos, C. A., Wang, T., & Yang, S. S. (2016) · Scientific Reports · doi:10.1038/srep19218 · Cited by 37
“This is especially true for very dilute and/or heterogeneous samples involved in many clinical and research scenarios 18–20 .”
BackgroundDeciphering the Draft Genome of Toxoplasma gondii RH Strain
Lau, Y. L., Lee, W.-C., Gudimella, R., Zhang, G., Ching, X. T., Razali, R., Aziz, F. A., Anwar, A., & Fong, M.-Y. (2016) · PLoS ONE · doi:10.1371/journal.pone.0157901 · Cited by 37
“The corrected reads were assembled using SOAPdenovo, a software that assembles 122 short oligonucleotide into contigs and scaffolds through de Bruijn graph algorithm [31].”
MethodBao, W., Qu, Y., Shan, X., & Wan, Y. (2016) · International Journal of Molecular Sciences · doi:10.3390/ijms17081198 · Cited by 38
Draft genome sequence of subterranean clover, a reference for genus Trifolium
Hirakawa, H., Kaur, P., Shirasawa, K., Nichols, P. G. H., Nagano, S., Appels, R., Erskine, W., & Isobe, S. (2016) · Scientific Reports · doi:10.1038/srep30358 · Cited by 39
Genomic Tools for the Enhancement of Vegetable Crops: A Case in Eggplant
Gramazio, P., Prohens, J., Plazas, M., Mangino, G., Herraiz, F., García‐Fortea, E., & Vilanova, S. (2017) · Notulae Botanicae Horti Agrobotanici Cluj-Napoca · doi:10.15835/nbha46110936 · Cited by 38
“The transcriptome of two other accessions ‘AE-P03’ and ‘LS1934’ was also sequenced to improve the de novo assembly (Li et al., 2010).”
BackgroundChen, Y., Sun, E., Song, J., Tong, Y., & Wu, B. (2018) · Canadian Journal of Microbiology · doi:10.1139/cjm-2017-0740 · Cited by 38
Wang, X., Zhou, H., Chen, D., Du, P., Lan, R., Qiu, X., Hou, X., Liu, Z., Sun, L., Xu, S., et al. (2019) · Journal of Clinical Microbiology · doi:10.1128/jcm.00683-19 · Cited by 38
“All good-quality paired-end reads were assembled into scaffolds using SOAPdenovo (16, 17).”
The genome of a subterrestrial nematode reveals adaptations to heat
Weinstein, D. J., Allen, S. E., Lau, M. C. Y., Erasmus, M., Asalone, K. C., Walters-Conte, K., Deikus, G. Y., Sebra, R., Borgonie, G., van Heerden, E., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-13245-8 · Cited by 38
Yin, M., Zhang, S., Du, X., Mateo, R. G., Guo, W., Li, A., Wang, Z., Wu, S., Chen, J., Liu, J., et al. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13363 · Cited by 41
“To estimate the genome size of M. ruthenica, clean Illumina reads were used to calculate the 21- K- mer distribution using SOAPdenovo (Li et al., 2010).”
MethodRates of genomic divergence in humans, chimpanzees and their lice
Johnson, K. P., Allen, J. M., Olds, B. P., Mugisha, L., Reed, D. L., Paige, K. N., & Pittendrigh, B. R. (2014) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2013.2174 · Cited by 38
Yan, J., Zhang, L., Wang, R.-Q., Xie, B., Xiao, L., Chen, R.-L., Guo, L.-X., & Xie, B. (2016) · International Journal of Molecular Sciences · doi:10.3390/ijms17010034 · Cited by 38
“The draft genome of PYd21 was assembled using a SOAPdenovo assembler [48] and is available under accession no.”
MethodConservation of Gene Cassettes among Diverse Viruses of the Human Gut
Minot, S. S., Wu, G. D., Lewis, J. D., & Bushman, F. D. (2012) · PLoS ONE · doi:10.1371/journal.pone.0042342 · Cited by 39
“tips, removing low-coverage links, resolving tiny repeats, and merging bubbles, were implemented as described in [25].”
MethodThompson, S. M., Johnson, C. P., Lu, A., Frampton, R. A., Sullivan, K. L., Fiers, M. W. E. J., Crowhurst, R. N., Pitman, A. R., Scott, I. A. W., Wen, A., et al. (2015) · Phytopathology · doi:10.1094/phyto-12-14-0363-fi · Cited by 38
“The filtered reads were assembled using SOAPdenovo (Li et al. 2010).”
MethodA vertebrate case study of the quality of assemblies derived from next-generation sequences
Liang, Y., Hillier, L. W., Minx, P. J., Thane, N., Locke, D. P., Martin, J. C., Chen, L., Mitreva, M., Miller, J. R., Haub, K. V., et al. (2011) · Genome biology · doi:10.1186/gb-2011-12-3-r31 · Cited by 37
“Our results have validated previous reports [1] that the assembly of large (>1 Gbp) vertebrate genomes is possible using both 454 and Illumina data.”
BackgroundMethodResultInfluentialJia, T., Wei, D., Meng, S., Allan, A. C., & Zeng, L. (2014) · PLoS ONE · doi:10.1371/journal.pone.0114568 · Cited by 37
“Using the SOAPdenovo software, we generated a total of 40,513 unigenes from the two samples.”
MethodThakur, K., Chawla, V., Bhatti, S., Swarnkar, M. K., Kaur, J., Shankar, R., & Jha, G. (2013) · PLoS ONE · doi:10.1371/journal.pone.0053937 · Cited by 37
“De novo assembling of high quality reads was performed using SOAPdenovo, ABySS and Velvet and in combination with a series of stepwise strategies [22], [23], [24], [27], [30].”
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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