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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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Genome Sequence of the Rice-Pathogenic Bacterium Acidovorax avenae subsp. avenae RS-1
Xie, G., Zhang, G., Liu, H., Lou, M.-M., Tian, W.-X., Li, B., Zhou, X., Zhu, B., & Jin, G. (2011) · Journal of Bacteriology · doi:10.1128/jb.05594-11 · Cited by 57
“Quality filtered reads were assembled in silico with SOAPdenovo and the GapCloser program (4).”
MethodWang, X., Zhao, Q., Luan, J., Wang, Y., Yan, G., & Liu, S. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-529 · Cited by 56
“Small K-mers made the graph very complex; while large K-mers have poor overlap in low sequencing depth regions [31].”
Human Microbiome Acquisition and Bioinformatic Challenges in Metagenomic Studies
D’Argenio, V. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19020383 · Cited by 56
“Specific assemblers have been developed for shotgun metagenomics (Table 1), such as SOAPdenovo [62], Velvet [63], MetaVelvet [64], Meta-IBDA [65], Genovo [66], Bambus2 [67], and Ray-Meta [68].”
MethodA chromosome‐level genome assembly of the parasitoid wasp Pteromalus puparum
Ye, X., Yan, Z., Yang, Y., Xiao, S., Chen, L., Wang, J., Wang, F., Xiong, S., Yang, M., Wang, F., et al. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13206 · Cited by 55
Self-citationde Castro, P. A., Chen, C., Almeida, R. S., Freitas, F. Z., Bertolini, M. C., Morais, E. R., Brown, N. A., Ramalho, L. N. Z., Hagiwara, D., Mitchell, T. K., et al. (2014) · Molecular Microbiology · doi:10.1111/mmi.12785 · Cited by 54
“21) alignment tool developed by BGI (Li et al., 2010) with a maximum of 2 mismatches allowed to accommodate polymorphisms between short reads and the © 2014 John Wiley & Sons Ltd, Molecular Microbiology, 94, 655–674 genome sequence.”
MethodBarrero, R. A., Napier, K. R., Cunnington, J. H., Liefting, L. W., Keenan, S., Frampton, R. A., Szabo, T., Bulman, S. R., Hunter, A. A., Ward, L. I., et al. (2017) · BMC Bioinformatics · doi:10.1186/s12859-016-1428-4 · Cited by 56
“We compared Velvet [16], SPAdes [17], ABySS [18] and SOAPdenovo [19] assemblers using twelve selected small RNA-Seq samples collected from distinct plant species generated in this study (Additional file 1).”
MethodGatzmann, F., Metzler, D., Krebs, S., Blum, H., Sing, A., Takano, A., Kawabata, H., Fingerle, V., Margos, G., & Becker, N. S. (2015) · Ticks and Tick-borne Diseases · doi:10.1016/j.ttbdis.2015.02.008 · Cited by 55
“Read filtering, de novo assembly with two assemblers (Li et al., 2010; Zerbino and Birney, 2008), alignment to the chromosome and plasmids cp26 and lp54 of reference sequence PBi (GenBank accession number NC 006156.1) (Glöckner et al., 2004) and SNP calling were performed using the Galaxy…”
MethodInfluentialWetzel, J. L., Kingsford, C., & Pop, M. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-95 · Cited by 55
“Our results hold across 360 ‘ ideal ’ sequencing experiments (see following section) as well as when using an off-the-shelf assembler in the presence of base-call errors (assembly of 8 bacterial genomes using SOAPdenovo [20]).”
ResultCao, Q., Didelot, X., Wu, Z., Li, Z., He, L., Li, Y., Ni, M., You, Y., Lin, X., Li, Z., et al. (2014) · Gut · doi:10.1136/gutjnl-2014-307345 · Cited by 56
Self-citationLiu, S., Chen, G., Xu, H., Zou, W.-B., Yan, W.-R., Wang, Q., Deng, H., Zhang, H., Yu, G., He, J., et al. (2016) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2016.07.033 · Cited by 55
Digital gene expression for non-model organismsPreprint
Hong, L. Z., Li, J., Schmidt‐Küntzel, A., Warren, W. C., & Barsh, G. S. (2011) · Genome Research · doi:10.1101/gr.122135.111 · Cited by 55
“Continuing advances in the cost and scale of sequencing technology and increased sophistication of de novo assembly algorithms are likely to provide reference genome sequences for thousands of mammalian species in the not too distant future (Zerbino and Birney 2008; Metzker 2009; Li et al. 2010; Robertson et al. 2010;…”
BackgroundZhang, J., Chen, L., Sun, S., Kudrna, D., Copetti, D., Li, W., Mu, T., Jiao, W., Xing, F., Lee, S., et al. (2016) · Scientific Data · doi:10.1038/sdata.2016.76 · Cited by 46
Zhao, M., Wang, W., Zhang, F., Ma, C., Liu, Z.-Q., Yang, M., Chen, W., Li, Q., Cui, M., Jiang, K., et al. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13332 · Cited by 53
Sequencing, Annotation, and Characterization of the Influenza Ferret Infectome
Leon, A. J., Banner, D., Xu, L., Ran, L., Peng, Z., Kang, Y., Chen, C., Xu, F., Huang, J., Zhao, Z. W., et al. (2012) · Journal of Virology · doi:10.1128/jvi.02476-12 · Cited by 54
“In this study, RNA samples were analyzed by next-generation sequencing (33), and the resulting 90-bp paired-end sequences were subjected to de novo assembly (25); this method resulted in the generation of sequence contigs by searching for overlapping regions among the short reads and using the paired-end information t…”
MethodGigabase-Scale Transcriptome Analysis on Four Species of Pearl Oysters
Huang, X., Zhao, M., Liu, W., Guan, Y.-Y., Shi, Y., Wang, Q., Wu, S.-Z., & He, M. (2012) · Marine Biotechnology · doi:10.1007/s10126-012-9484-x · Cited by 54
“Sequence Assembly and Annotation Raw sequence data after filtering dirty raw reads was carried out with short reads assembling program—SOAPdenovo (Li et al. 2010b) (http://soap.genomics.org.cn/soapdenovo.html).”
InfluentialTulin, S., Aguiar, D., Istrail, S., & Smith, J. (2013) · EvoDevo · doi:10.1186/2041-9139-4-16 · Cited by 55
“In the last few years several assembly algorithms have been released to meet these challenges: Trans-ABySS [25], SOAPdenovo [26], Velvet/Oases [27,28], and Trinity [29].”
MethodGenome Sequence of the Oleaginous Red Yeast Rhodosporidium toruloides MTCC 457
Kumar, S., Kushwaha, H., Bachhawat, A. K., Raghava, G. P. S., & Ganesan, K. (2012) · Eukaryotic Cell · doi:10.1128/ec.00156-12 · Cited by 54
Eichmeier, A., Komínková, M., Komínek, P., & Baránek, M. (2016) · PLoS ONE · doi:10.1371/journal.pone.0167966 · Cited by 54
Day, J., Seet, Q., Thanh, L. T., Trieu, P. H., Van, A. D., Hoang, T. N., Chau, T. T. H., Lan, N. P. H., Châu, N. V. V., Ashton, P., et al. (2017) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0005628 · Cited by 54
Rao, S., & Nandineni, M. R. (2017) · PLoS ONE · doi:10.1371/journal.pone.0183567 · Cited by 55
Zhang, X., Yao, D., Wang, Q., Xu, W., Wei, Q., Wang, C., Liu, C., Zhang, C., Hong, Y., Ling, Y., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0054762 · Cited by 53
“The cotton whole-genome sequencing results are not publically available, thus the de novo assembly was carried out using SOAPdenovo, a short reads assembling program [66].”
MethodInfluentialFan, P., Nie, L., Jiang, P., Feng, J., Lv, S., Chen, X., Bao, H., Guo, J., Tai, F., Wang, J., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0080595 · Cited by 55
“De novo assembly of the transcriptome sequence was performed using the short reads assembling program SOAPdenovo [29] (version 1.”
MethodInfluentialSelf-citationCalderón, C. E., Ramos, C., de Vicente, A., & Cazorla, F. M. (2015) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-10-14-0326-fi · Cited by 48
Zhu, J., Zhao, N., & Yang, B. (2012) · PLoS ONE · doi:10.1371/journal.pone.0032291 · Cited by 53
“Raw reads were then assembled into sequence contigs, scaffolds, and unigenes using SOAPdenovo software [13], and clustered using TGI Clustering tools [14].”
MethodWelch, A. J., Collins, K., Ratan, A., Drautz‐Moses, D. I., Schuster, S. C., & Lindqvist, C. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.02.024 · Cited by 54
“05 (Li et al., 2010).”
Unraveling the message: insights into comparative genomics of the naked mole-rat
Lewis, K. N., Soifer, I., Melamud, E., Roy, M. A., McIsaac, R. S., Hibbs, M., & Buffenstein, R. (2016) · Mammalian Genome · doi:10.1007/s00335-016-9648-5 · Cited by 53
“Indeed the various nutrient-sensing genes shown to modulate longevity (e.g., insulin/IGF-1, FOXO, mTOR) appear to regulate resource allocation for somatic maintenance and thereby influence survival [reviewed in (Kapahi 2010)].”
BackgroundMethodInfluentialGenetic and Genomic Tools forCannabis sativa
Vergara, D., Baker, H., Clancy, K., Keepers, K. G., Mendieta, J. P., Pauli, C. S., Tittes, S. B., White, K. H., & Kane, N. C. (2016) · Critical Reviews in Plant Sciences · doi:10.1080/07352689.2016.1267496 · Cited by 58
“Sequences were assembled de novo using SOAPdenovo (Li et al., 2010).”
MethodDeng, C. H., Plummer, K. M., Jones, D., Mesarich, C. H., Shiller, J. B., Taranto, A. P., Robinson, A. J., Kastner, P., Hall, N. E., Templeton, M. D., et al. (2017) · BMC Genomics · doi:10.1186/s12864-017-3699-1 · Cited by 55
“12) [145] then scaffolded using SSPACE with MP reads (SSPACE version 2) [147].”
MethodThe “wildness” of the giant panda gut microbiome and its relevance to effective translocation
Yao, R., Xu, L., Hu, T., Chen, H., Qi, D., Gu, X., Yang, X., Yang, Z., & Zhu, L. (2019) · Global Ecology and Conservation · doi:10.1016/j.gecco.2019.e00644 · Cited by 52
Paired-end sequencing of Fosmid libraries by IlluminaPreprint
Williams, L., Tabbaa, D., Li, N., Berlin, A. M., Shea, T., MacCallum, I., Lawrence, M. S., Drier, Y., Getz, G. A., Young, S., et al. (2012) · Genome Research · doi:10.1101/gr.138925.112 · Cited by 55
“However, early short-read assemblies of complex genomes, including human genomes, turned out fragmented – despite jumps up to ~12 kb in length (Li et al. 2010a; Li et al. 2010b; Schuster et al. 2010; Yan et al. 2011).”
BackgroundZhao, C., & Eun, J. (2020) · Food Research International · doi:10.1016/j.foodres.2020.109030 · Cited by 51
Prakash, B., Singh, P. P., Gupta, V. K., & Raghuvanshi, T. S. (2023) · Food and Chemical Toxicology · doi:10.1016/j.fct.2023.114241 · Cited by 52
Yao, B., Zhao, Y., Wang, Q., Zhang, M., Liu, M., Liu, H., & Li, J. (2011) · Molecular and Cellular Biochemistry · doi:10.1007/s11010-011-1209-3 · Cited by 52
“The reads obtained were randomly clipped into 29 bp K-mers for assembly using de Bruijn graph and SOAPdenovo software [7].”
MethodGenetic anchoring of whole-genome shotgun assemblies
Mascher, M., & Stein, N. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00208 · Cited by 55
“Next-generation sequencing (NGS) has facilitated the rapid collection of vast amounts of genomic sequence data, enabling whole-genome shotgun (WGS) assemblies in species with huge genomes (Li et al., 2010; Jia et al., 2013; Ling et al., 2013; Nystedt et al., 2013).”
BackgroundXie, M., Huang, Y., Zhang, Y., Wang, X., Yang, H., Yu, O. S., Dai, W., & Fang, C. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-823 · Cited by 54
“The de Bruijn graph was firstly used to generate contigs [34].”
MethodSelf-citationMeng, J., & Bowser, M. T. (2013) · Analytical Chemistry · doi:10.1021/ac401875h · Cited by 53
Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis
Ye, Y., & Tang, H. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv510 · Cited by 52
“Contact: yye@indiana.edu”
Targeted Assembly of Short Sequence Reads
Warren, R. L., & Holt, R. A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0019816 · Cited by 52
“This is accomplished best by whole-genome de novo assembly methods [16,18] and alignmentguided targeted assemblies.”
BackgroundMethodHernández, D., Tewhey, R., Veyrieras, J., Farinelli, L., Østerås, M., François, P., & Schrenzel, J. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt590 · Cited by 52
“The obtained structure corresponds to the overlaps graph analog version of the repeat graph that was first described in Pevzner and Tang (2001). Other structures that follow the same principle are the string graph (Myers, 2005) and the unipath graph (Butler et al.”
Zhou, M., Guo, P., Wang, T., Gao, L., Yin, H., Cai, C., Gu, J., & Lü, X. (2017) · Biotechnology for Biofuels · doi:10.1186/s13068-017-0885-y · Cited by 52
“The redundant ORFs were removed by CD-HIT [13] from the non-redundant gene catalog and the abundances were annotated by SOAPaligner [22].”
MethodTang, D., Liu, L.-L., He, Q.-R., Wen, Y., Li, D., & Gao, J. (2018) · Journal of Natural Products · doi:10.1021/acs.jnatprod.8b00203 · Cited by 52
Oleksyk, T. K., Pombert, J., Siu, D., Mazo‐Vargas, A., Ramos, B., Guiblet, W. M., Afanador, Y., Ruiz-Rodriguez, C., Nickerson, M. L., Logue, D. M., et al. (2012) · GigaScience · doi:10.1186/2047-217x-1-14 · Cited by 51
“DS performed sequencing and assembly by SOAPdenovo.”
MethodInfluentialDe novo likelihood-based measures for comparing genome assemblies
Ghodsi, M., Hill, C. M., Astrovskaya, I., Lin, H., Sommer, D. D., Koren, S., & Pop, M. (2013) · BMC Research Notes · doi:10.1186/1756-0500-6-334 · Cited by 51
“We focus here on SOAPdenovo assemblies of the Escherichia coli K12 MG1655 genome (Figure 5).”
MethodInfluentialZheng, T., Li, P., Zhuo, X., Liu, W., Qiu, L., Li, L., Yuan, C., Sun, L., Zhang, Z., Wang, J., et al. (2021) · New Phytologist · doi:10.1111/nph.17894 · Cited by 51
“All the contigs of the Oxford Nanopore long reads were extended using SMART DENOVO to generate an assembly with a total contig length of 237.7 Mb (91% of the genome), consisting of 225 contigs with a contig N50 size of 2.75 Mb, and the largest contig size was 12.6 Mb (Tables S3, S6).”
InfluentialSelf-citationLellek, H., Franke, G. C., Ruckert, C., Wolters, M., Wolschke, C., Christner, M., Büttner, H., Alawi, M., Kröger, N., & Rohde, H. (2015) · International Journal of Medical Microbiology · doi:10.1016/j.ijmm.2015.09.005 · Cited by 51
Insights into the Loblolly Pine Genome: Characterization of BAC and Fosmid Sequences
Wegrzyn, J., Lin, B. Y., Zieve, J. J., Dougherty, W. M., Martínez‐García, P. J., Koriabine, M., Holtz-Morris, A. E., deJong, P. J., Crepeau, M., Langley, C. H., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0072439 · Cited by 53
Gao, S., Duan, A., Xu, W., Yu, P., Hang, L., Houk, K. N., & Tang, Y. (2016) · Journal of the American Chemical Society · doi:10.1021/jacs.6b01528 · Cited by 51
Genomic insights into a robust gamma-aminobutyric acid-producer Lactobacillus brevis CD0817
Gao, D., Chang, K., Ding, G., Wu, H., Chen, Y., Jia, M., Liu, X., Wang, S., Jin, Y., Pan, H., et al. (2019) · AMB Express · doi:10.1186/s13568-019-0799-0 · Cited by 54
“The filtered reads were de novo assembled by SOAPdenovo (Li et al. 2010; Luo et al. 2012) (http://soap.”
Bekkevold, D., Höjesjö, J., Nielsen, E. E., Aldvén, D., Als, T. D., Sodeland, M., Kent, M., Lien, S., & Hansen, M. M. (2019) · Evolutionary Applications · doi:10.1111/eva.12877 · Cited by 51
“Reads from the 16 individuals were aligned to the reference using BWA (Li & Durbin, 2009); putative SNPs within each individual were identi‐ fied using SAMtools (Li et al., 2009).”
MethodCharacteristics of Gut Microbiota in Patients with GH-Secreting Pituitary Adenoma
Lin, B. C., Wang, M., Gao, R., Ye, Z., Yu, Y., He, W., Qiao, N., Ma, Z., Ji, C., Shi, C., et al. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.00425-21 · Cited by 49
Self-citationWang, W., He, X., Yan, X., Ma, B., Lu, C., Wu, J., Zheng, Y., Wang, W., Xue, W., Tian, X., et al. (2023) · New Phytologist · doi:10.1111/nph.18814 · Cited by 49
Lee, W. S., Gudimella, R., Wong, G. R., Tammi, M. T., Khalid, N., & Harikrishna, J. A. (2015) · PLoS ONE · doi:10.1371/journal.pone.0127526 · Cited by 50
“html) [57].”
Zhang, J., Xie, P., Lascoux, M., Meagher, T. R., & Liu, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0066370 · Cited by 50
“De novo assembly was carried out by SOAPdenovo, a genome assembly program developed specifically for next-generation short-read sequences [27].”
MethodA draft genome sequence of an invasive mosquito: an ItalianAedes albopictus
Dritsou, V., Topalis, P., Windbichler, N., Simoni, A., Hall, A., Lawson, D., Hinsley, M., Hughes, D., Napolioni, V., Crucianelli, F., et al. (2015) · Pathogens and Global Health · doi:10.1179/2047773215y.0000000031 · Cited by 51
Unusually Large Number of Mutations in Asexually Reproducing Clonal Planarian Dugesia japonica
Nishimura, O., Hosoda, K., Kawaguchi, E., Yazawa, S., Hayashi, T., Inoue, T., Umesono, Y., & Agata, K. (2015) · PLoS ONE · doi:10.1371/journal.pone.0143525 · Cited by 50
“01 [63] based on the k-mer frequency spectrum (KFS) algorithm.”
MethodGao, F., Wang, N., Li, H., Liu, J., Fu, C., Xiao, Z., Wei, C., Lu, X., Feng, J., & Zhou, Y. (2016) · Scientific Reports · doi:10.1038/srep34601 · Cited by 50
Chen, Y., Sun, E., Song, J., Yang, L., & Wu, B. (2018) · Current Microbiology · doi:10.1007/s00284-017-1419-3 · Cited by 50
Ren, X., Cao, S., Akami, M., Mansour, A., Yang, Y., Jiang, N., Wang, H., Zhang, G., Qi, X., Xu, P., et al. (2022) · BMC Biology · doi:10.1186/s12915-022-01399-9 · Cited by 48
“io/ megab ox/) with the default parameter of k-mer sizes of 27 to 127; therefore, contigs/ scaffolds were constructed and assessed based on a De Bruijn graph (Additional file 1: Table S1) [82].”
MethodPan, X. D., Chang, Y., Li, C., Qiu, X., Cui, X., Meng, F., Zhang, S., Li, X., & Lu, S. (2023) · Horticulture Research · doi:10.1093/hr/uhad069 · Cited by 49
“3), Geneid [48], Genescan [49], GlimmerHMM [50], and SNAP [51] were used in ab initio gene prediction pipeline.”
MethodInfluentialGarcía-López, R., Vázquez-Castellanos, J. F., & Moyá, A. (2015) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2015.00141 · Cited by 49
“Assemblers use different approaches to generate larger sequences from the reads but they can be classified into two main types: overlap layout consensus (OLC) and de Bruijn assemblers (Li et al., 2010).”
MethodWang, C., Gao, C., Wang, L., Zheng, L., Yang, C., & Wang, Y. (2013) · Plant Molecular Biology · doi:10.1007/s11103-013-0124-2 · Cited by 49
“html) (Li et al. 2010), and the longest assembled sequences without Ns are”
BackgroundMethodNext Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows
Torri, F., Dinov, I. D., Zamanyan, A., Hobel, S., Genco, A., Petrosyan, P., Clark, A. P., Liu, Z., Eggert, P., Pierce, J., et al. (2012) · Genes · doi:10.3390/genes3030545 · Cited by 51
“De Bruijn graphs algorithm is used by most assemblers (Velvet [19], SOAPdeNOVO [20], ABySS [21]) and reduces the computational charge by breaking reads into smaller sub-sequences of DNA, called k-mers, where the k parameter describes the length in bases of these sequences [22] .”
MethodIMG/M-HMP: A Metagenome Comparative Analysis System for the Human Microbiome Project
Markowitz, V. M., Chen, I.-M. A., Chu, K., Szeto, E., Palaniappan, K., Jacob, B., Ratner, A., Liolios, K., Pagani, I., Huntemann, M., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0040151 · Cited by 51
“Louis), and then processed using the SOAP denovo for assembly [20] and a MetaGenemark for predicting genes, as described in detail in [17].”
MethodA de novo metagenomic assembly program for shotgun DNA reads
Lai, B., Ding, R., Li, Y., Duan, L., & Zhu, H. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts162 · Cited by 49
“The de Brujin graph-based assemblers, which are more suitable for shorter reads ( 100 bp), such as Velvet (Zerbinor et al., 2008), SOAPdenovo (Li et al., 2010) and Meta- IDBA (Peng et al., 2011), are not included in the comparisons with MAP in this work, as they are less preferred when compared with the graph-based as…”
Self-citationHe, S., Ding, L., Li, K., Hu, H., Ye, L., & Ren, H. (2017) · Bioresource Technology · doi:10.1016/j.biortech.2017.09.026 · Cited by 49
Priya, G., Lau, N., Furusawa, G., Balachandra, D., Foong, S. Y., & Amirul, A.-A. A. (2018) · Agri Gene · doi:10.1016/j.aggene.2018.07.001 · Cited by 49
Asante, J., & Sekyere, J. O. (2019) · Environmental Microbiology Reports · doi:10.1111/1758-2229.12735 · Cited by 51
The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development
Li, M., Yang, S., Xu, W., Pu, Z., Feng, J., Wang, Z., Zhang, C., Peng, M., Du, C., Lin, F., et al. (2019) · BMC Plant Biology · doi:10.1186/s12870-019-1708-z · Cited by 51
Self-citationKim, M., Xi, H., & Park, J. (2021) · PLoS ONE · doi:10.1371/journal.pone.0252181 · Cited by 49
Lu, M., Ngou, F.-H., Chao, Y., Lai, Y., Chen, N.-Y., Lee, F.-Y., & Chiou, P. P. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-651 · Cited by 50
“After sequencing, the SOAP de novo software [23] was used to assemble the data.”
MethodA draft genome assembly of spotted hyena, Crocuta crocuta
Yang, C., Li, F., Xiong, Z., Koepfli, K., Ryder, O. A., Perelman, P. L., Li, Q., & Zhang, G. (2020) · Scientific Data · doi:10.1038/s41597-020-0468-9 · Cited by 49
The Battle to Sequence the Bread Wheat Genome: A Tale of the Three Kingdoms
Guan, J., Garcia, D. F., Zhou, Y., Appels, R., Li, A., & Mao, L. (2020) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2019.09.005 · Cited by 48
“05) [30] was used to assemble the filtered short reads (<100 bp) achieving contigs with an N50 of 4.”
MethodLiao, Q., Du, R., Gou, J., Guo, L., Shen, H., Liu, H., Nguyen, J. K., Ming, R., Yin, T., Huang, S., et al. (2020) · The Plant Journal · doi:10.1111/tpj.15009 · Cited by 53
Detecting Superbubbles in Assembly Graphs
Onodera, T., Sadakane, K., & Shibuya, T. (2013) · Lecture notes in computer science · doi:10.1007/978-3-642-40453-5_26 · Cited by 48
“After obtained the unipath graph, many sequencing algorithms next detect simple typical motif structures caused by errors to detect errors: The most common motifs are tips, bubbles, and cross links [4,6,15,17] (Fig.”
MethodApplication of second-generation sequencing to cancer genomics
Robison, K. E. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbq013 · Cited by 48
“requires enormous compute resources [33] and is”
BackgroundComparative Phylogenomics of Pathogenic and Nonpathogenic Species
Whiston, E., & Taylor, J. W. (2015) · G3 Genes Genomes Genetics · doi:10.1534/g3.115.022806 · Cited by 48
“GenomeswereassembledusingtheSOAPdenovopipeline(Li et al. 2010): corrector, SOAPdenovo, GapCloser.”
Ji, X., Mo, K.-Q., Ren, L., Li, G.-L., Huang, J., & Huang, H. (2015) · Genome Announcements · doi:10.1128/genomea.00819-15 · Cited by 48
“The raw sequence data comprise a total of 61,950,544 reads, assembled into 1,608 contigs through the SOAPdenovo alignment tool (14, 15).”
MethodWhole Genome Re-sequencing Reveals Natural Variation and Adaptive Evolution of Phytophthora sojae
Zhang, X., Liu, B., Zou, F., Shen, D., Yin, Z., Wang, R., He, F., Wang, Y., Tyler, B. M., Fan, W., et al. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.02792 · Cited by 48
Self-citationGenomic signatures of high-altitude adaptation and chromosomal polymorphism in geladas
Chiou, K. L., Janiak, M. C., Schneider‐Crease, I. A., Sen, S., Ayele, F., Chuma, I. S., Knauf, S., Lemma, A., Signore, A. V., D’Ippolito, A. M., et al. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01703-4 · Cited by 52
Mardi, M., Farsad, L. K., Gharechahi, J., & Salekdeh, G. H. (2015) · PLoS ONE · doi:10.1371/journal.pone.0130425 · Cited by 48
“Transcriptome de novo assembly was performed using the SOAP de novo software [32].”
MethodWang, B., Ekblom, R., Bunikis, I., Siitari, H., & Höglund, . (2014) · BMC Genomics · doi:10.1186/1471-2164-15-180 · Cited by 48
“05 (63mer version) [58] with default settings (Additional file 4).”
BackgroundCai, G., Leadbetter, C. W., Muehlbauer, M., Molnar, T. J., & Hillman, B. I. (2013) · PLoS ONE · doi:10.1371/journal.pone.0082408 · Cited by 47
“The genome was assembled with SOAPdenovo [29] using the trimmed and filtered reads.”
MethodInfluentialHawkeye and AMOS: visualizing and assessing the quality of genome assemblies
Schatz, M. C., Phillippy, A. M., Sommer, D. D., Delcher, A. L., Puiu, D., Narzisi, G., Salzberg, S. L., & Pop, M. (2011) · Briefings in Bioinformatics · doi:10.1093/bib/bbr074 · Cited by 47
“In the top figure one can immediately see that with this short read data set and for the parameters used, ABySS [26] produced the best assembly overall followed by SUTTA [27], SOAPdenovo [28] and Velvet.”
MethodDiversity of nitrogen assimilation pathways among microbial photosynthetic eukaryotes
Terrado, R., Monier, A., Edgar, R. E., & Lovejoy, C. (2015) · Journal of Phycology · doi:10.1111/jpy.12292 · Cited by 48
“Scaffolding was then performed using a combination of BWA and ABySS, followed by gap closing using SOAPdenovo GapCloser (Li et al. 2010a,b).”
MethodMira, N. P., Münsterkötter, M., Dias-Valada, F., Santos, J., Palma, M., Roque, F. C., Guerreiro, J. F., Rodrigues, F. J. S., Sousa, M. J., Leão, C., et al. (2014) · DNA Research · doi:10.1093/dnares/dst058 · Cited by 47
An introduction to plant phylogenomics with a focus on palms
Barrett, C. F., Bacon, C. D., Antonelli, A., Cano, Á., & Hofmann, T. (2016) · Botanical Journal of the Linnean Society · doi:10.1111/boj.12399 · Cited by 46
“…& Birney, © 2016 The Linnean Society of London, Botanical Journal of the Linnean Society, 2016, 182, 234–255 Downloaded from https://academic.oup.com/botlinnean/article-abstract/182/2/234/2707814 by guest on 28 July 2018 2008; Simpson et al., 2009; Li et al., 2010; see Bradnam et al., 2013).”
BackgroundLi, D., Wang, X., Deng, Z., Liu, H., Yang, H. Y., & He, G. (2016) · Scientific Reports · doi:10.1038/srep23540 · Cited by 47
Self-citationXie, J., Li, S., Mo, C., Xiao, X., Peng, D., Wang, G., & Xiao, Y. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.01084 · Cited by 49
“A draft genome sequence was assembled on the basis of the high-quality reads using the de novo assembler SOAPdenovo (Li et al., 2010).”
MethodInfluentialSelf-citationHidden genomic evolution in a morphospecies—The landscape of rapidly evolving genes in Tetrahymena
Xiong, J., Yang, W., Chen, K., Jiang, C., Ma, Y., Chai, X., Yan, G., Wang, G., Yuan, D., Liu, Y., et al. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000294 · Cited by 47
“MAC genomes of each species were assembled using SOAPdenovo [84] or ALLPATHS-LG [85].”
MethodGenome-wide genetic variations are highly correlated with proximal DNA methylation patternsPreprint
Qü, W., Hashimoto, S., Shimada, A., Nakatani, Y., Ichikawa, K., Saito, T., Ogoshi, K., Matsushima, K., Suzuki, Y., Sugano, S., et al. (2012) · Genome Research · doi:10.1101/gr.140236.112 · Cited by 47
“Estimation of the ancestor sequence of Hd-rR and HNI was given by multiple alignments using an out-group medaka strain HSOK which was assembled using the SOAPdenovo assembler (Li et al. 2010).”
MethodChromosome-scale genome assembly of the brown anole (Anolis sagrei), an emerging model species
Geneva, A. J., Park, S., Bock, D. G., de Mello, P. L. H., Sarigol, F., Tollis, M., Donihue, C. M., Reynolds, R. G., Feiner, N., Rasys, A. M., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-04074-5 · Cited by 50
Xu, L., Wu, M., & Han, Z. (2013) · PLoS ONE · doi:10.1371/journal.pone.0079443 · Cited by 46
“Transcriptome de novo assembly of the clean reads was performed with the short read assembly program SOAPdenovo [44].”
MethodMultidrug-resistant Citrobacter freundii ST139 co-producing NDM-1 and CMY-152 from China
Yang, L., Li, P., Liang, B., Hu, X., Xie, J., Xie, J., Yang, C., Hao, R., Wang, L., Jia, L., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-28879-9 · Cited by 46
Yang, Y., Li, X., Kong, X., Ma, L., Hu, X., & Yang, Y. (2014) · Functional & Integrative Genomics · doi:10.1007/s10142-014-0419-7 · Cited by 45
Memory efficient minimum substring partitioning
Li, Y., Kamousi, P., Han, F., Yang, S., Yan, X., & Suri, S. (2013) · Proceedings of the VLDB Endowment · doi:10.14778/2535569.2448951 · Cited by 45
“With the development of next-generation sequencing techniques, the de Bruijn graph sequence assembly approaches became popular, including Euler[18], Velvet[26], AllPaths[5], SOAPdenovo[12], etc.”
BackgroundMethodResultInfluentialSelf-citationPE-Assembler: de novo assembler using short paired-end reads
Ariyaratne, P. N., & Sung, W.-K. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq626 · Cited by 45
“Received on June 4, 2010; revised on October 18, 2010; accepted on October 29, 2010”
BackgroundInsights into novel antimicrobial compounds and antibiotic resistance genes from soil metagenomes
de Castro, A. P., Fernandes, G. D. R., & Franco, O. L. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00489 · Cited by 46
“The assembly procedure also leads to better gene prediction: 81842 genes predicted from MetaVelvet scaffolds, 38445 and 65176 predicted genes from Velvet, and SOAPdenovo scaffolds, respectively, (Namiki et al., 2012).”
MethodInfluentialMATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels
Marschall, T., Hajirasouliha, I., & Schönhuth, A. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt556 · Cited by 45
Sesterterpene ophiobolin biosynthesis involving multiple gene clusters in Aspergillus ustus
Chai, H., Yin, R., Liu, Y., Meng, H., Zhou, X., Zhou, G., Bi, X., Yang, X. W., Zhu, T., Zhu, W., et al. (2016) · Scientific Reports · doi:10.1038/srep27181 · Cited by 45
Li, X., Du, Y., Du, P., Dai, H., Fang, Y., Li, Z., Lv, N., Zhu, B., Kan, B., & Wang, D. (2016) · Scientific Reports · doi:10.1038/srep37372 · Cited by 45
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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