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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
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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
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“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
Cited by
Sorted by citations
Items 201–300 of 1,002
Building the sequence map of the human pan-genome
Li, R., Li, Y., Zheng, H., Luo, R., Zhu, H., Li, Q., Qian, W., Ren, Y., Tian, G., Li, J., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1596 · Cited by 261
Self-citationChen, S., Yang, P., Jiang, F., Wei, Y., Ma, Z., & Kang, L. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015633 · Cited by 257
“Assembly De novo assembly of the short reads was performed using SOAPdenovo [25] as follows.”
MethodLong-read sequencing and de novo assembly of a Chinese genome
Shi, L., Guo, Y., Dong, C., Huddleston, J., Yang, H., Han, X., Fu, A., Li, Q., Li, N., Gong, S., et al. (2016) · Nature Communications · doi:10.1038/ncomms12065 · Cited by 259
“(c) Shared SNVs discovered in HX1, AK1, HuRef, NA12878 and YH.”
BackgroundResultInfluentialSelf-citationMarcet‐Houben, M., Ballester, A., de la Fuente, B., Harries, E., Marcos, J. F., González-Candelas, L., & Gabaldón, T. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-646 · Cited by 250
“Gaps were then filled in using Gapcloser [57].”
MethodZhang, W., Chen, J., Yang, Y., Tang, Y., Shang, J., & Shen, B. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017915 · Cited by 250
“However, short reads from eukaryote genomes, with features of gargantuan size and high repetitiveness, make sky-high requirement for assembly strategies and computer hardware [10,11,23,24].”
BackgroundMethodInfluentialA survey of error-correction methods for next-generation sequencing
Yang, X. F., Chockalingam, S. P., & Aluru, S. (2012) · Briefings in Bioinformatics · doi:10.1093/bib/bbs015 · Cited by 249
“A similar idea is also used as a stand-alone error-correction component in the SOAPdenovo assembler [23].”
MethodInfluentialLi, D., Deng, Z., Qin, B., Liu, X., & Men, Z. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-192 · Cited by 248
“However, of the 22,756 unigenes, more than 0.8% unigenes had a coverage depth of less than 1, which was partly due to the drawback to the de Bruijn graph approach used in SOAPdenovo program [76].”
MethodInfluentialThe genome and transcriptome of Japanese flounder provide insights into flatfish asymmetry
Shao, C., Bao, B., Xie, Z., Chen, X., Li, B., Jia, X., Yao, Q., Ortı́, G., Li, W., Li, X., et al. (2016) · Nature Genetics · doi:10.1038/ng.3732 · Cited by 248
Self-citationMa, P.-F., Zhang, Y.-X., Zeng, C., Guo, Z., & Li, D.-Z. (2014) · Systematic Biology · doi:10.1093/sysbio/syu054 · Cited by 244
Genome Sequence of the Tsetse Fly ( Glossina morsitans ): Vector of African Trypanosomiasis
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The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus
Schwarz, E. M., Korhonen, P. K., Campbell, B. E., Young, N. D., Jex, A. R., Jabbar, A., Hall, R. S., Mondal, A., Howe, A., Pell, J., et al. (2013) · Genome biology · doi:10.1186/gb-2013-14-8-r89 · Cited by 248
Tian, C. F., Zhou, Y., Zhang, Y., Li, Q. Q., Zhang, Y., Li, D. F., Wang, S., Wang, J., Gilbert, L. B., Li, Y. R., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1120436109 · Cited by 246
“Assembly was done with SOAPdenovo (38).”
Self-citationGiampetruzzi, A., Roumi, V., Roberto, R., Malossini, U., Yoshikawa, N., Notte, P. L., Terlizzi, F., Credi, R., & Saldarelli, P. (2011) · Virus Research · doi:10.1016/j.virusres.2011.10.010 · Cited by 242
Wang, J., Qi, J., Zhao, H., He, S. C., Zhang, Y., Wei, S., & Zhao, F. (2013) · Scientific Reports · doi:10.1038/srep01843 · Cited by 244
Self-citationVollmers, J., Wiegand, S., & Kaster, A.-K. (2017) · PLoS ONE · doi:10.1371/journal.pone.0169662 · Cited by 240
Teo, S. M., Yudi Pawitan, Y., Ku, C., Chia, K. S., & Salim, A. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts535 · Cited by 246
“It is difficult to judge which method is superior although the methods developed more recently such as SOAPdenovo (Li et al., 2010) claims faster computation time and longer contig size and assembly accuracy when compared to earlier methods such as ABySS (Simpson et al., 2009) and velvet (Zerbino…”
MethodInfluentialThe allotetraploid origin and asymmetrical genome evolution of the common carp Cyprinus carpio
Xu, P., Xu, J. H., Liu, G., Chen, L., Zhou, Z., Peng, W., Jiang, Y., Zhao, Z., Jia, Z., Sun, Y., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12644-1 · Cited by 248
Zhang, J., Liang, S., Duan, J., Wang, J., Chen, S., Cheng, Z., Zhang, Q., Liang, X., & Li, Y. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-90 · Cited by 234
“The samples were assembled with SOAPdenovo [29] separately.”
MethodSelf-citationEfficient de novo assembly of single-cell bacterial genomes from short-read data sets
Chitsaz, H., Yee-Greenbaum, J. L., Tesler, G., Lombardo, M., Dupont, C. L., Badger, J. H., Novotny, M. A., Rusch, D. B., Fraser, L. J., Gormley, N. A., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1966 · Cited by 240
Nygaard, S., Zhang, G., Schiøtt, M., Li, C., Wurm, Y., Hu, H., Zhou, J., Ji, L., Qiu, F., Rasmussen, M. A., et al. (2011) · Genome Research · doi:10.1101/gr.121392.111 · Cited by 236
Self-citationHigh genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus
Zheng, W., Huang, L., Huang, J., Wang, X., Chen, X., Zhao, J., Guo, J., Zhuang, H., Qiu, C., Liu, J., et al. (2013) · Nature Communications · doi:10.1038/ncomms3673 · Cited by 235
Self-citationConDeTri - A Content Dependent Read Trimmer for Illumina Data
Smeds, L., & Künstner, A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0026314 · Cited by 226
“Popular short read de novo assemblers like VELVET [7] or SOAPDENOVO [8] use the latter approach whereas genome assemblers developed for Sanger or 454 data like CABOG [9] or NEWBLER [10] use the overlappingconsensus technique.”
BackgroundInfluentialAn Overview of Genome Organization and How We Got There: from FISH to Hi-C
Fraser, J., Williamson, I., Bickmore, W. A., & Dostie, J. (2015) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00006-15 · Cited by 232
“Even though high sequence coverage is now possible with deep sequencing technologies, the small size and generally low quality of the reads render assembly difficult and result most often in fragmented genome maps, particularly for large and repeat-rich genomes (325, 326).”
BackgroundGenomic Analyses Reveal Potential Independent Adaptation to High Altitude in Tibetan Chickens
Wang, M., Li, Y., Peng, M., Zhong, L., Wang, Z., Li, Q., Tu, X.-L., Dong, Y., Zhu, C., Wang, L., et al. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv071 · Cited by 225
“Reads, after quality filtration, were assembled by SOAPdenovo with the processes of contig construction, gap filling, and scaffold construction (Li et al. 2010).”
MethodSelf-citationPanax ginseng genome examination for ginsenoside biosynthesis
Xu, J., Chu, Y., Liao, B., Xiao, S., Yin, Q., Bai, R., Su, H., Dong, L., Li, X., Qian, J., et al. (2017) · GigaScience · doi:10.1093/gigascience/gix093 · Cited by 223
“Finally, the small-insert libraries were used for gap closure of the scaffolds using GapCloser (GapCloser, RRID:SCR 015026) [52].”
Yang, C., Chowdhury, D., Zhang, Z., Cheung, W. K., Lü, A., Bian, Z., & Zhang, L. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.11.028 · Cited by 242
Dissection of the Octoploid Strawberry Genome by Deep Sequencing of the Genomes of Fragaria Species
Hirakawa, H., Shirasawa, K., Kosugi, S., Tashiro, K., Nakayama, S., Yamada, M., Kohara, M., Watanabe, A., Kishida, Y., Fujishiro, T., et al. (2013) · DNA Research · doi:10.1093/dnares/dst049 · Cited by 226
Feng, C., Chen, M., Xu, C., Bai, L., Yin, X.-R., Li, X., Allan, A. C., Ferguson, I. B., & Chen, K. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-19 · Cited by 228
“04) [52] at the parameters of “-K 29 -M 2 -L 50” by BGI.”
Paragraph: a graph-based structural variant genotyper for short-read sequence data
Chen, S., Krusche, P., Dolzhenko, E., Sherman, R. M., Petrovski, R., Schlesinger, F., Kirsche, M., Bentley, D. R., Schatz, M. C., Sedlazeck, F. J., et al. (2019) · Genome Biology · doi:10.1186/s13059-019-1909-7 · Cited by 196
Johnson, M. T. J., Carpenter, E. J., Tian, Z., Bruskiewich, R., Burris, J. N., Carrigan, C. T., Chase, M. W., Clarke, N. D., Covshoff, S., dePamphilis, C. W., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0050226 · Cited by 218
“Finally, the rapidly changing methods associated with sequencing platforms and chemistry will likely have large, but as of yet, unquantified effects on sequencing success [21,22].”
MethodZhang, Y., Du, L., Liu, A., Chen, J., Wu, L.-W., Hu, W., Zhang, W., Kim, K., Lee, S.-C., Yang, T., et al. (2016) · Frontiers in Plant Science · doi:10.3389/fpls.2016.00306 · Cited by 221
Zhou, F., Cao, H., Zuo, X., Zhang, T., Zhang, X., Liu, X., Xu, R., Chen, G., Zheng, X., Zheng, X., et al. (2016) · Nature Genetics · doi:10.1038/ng.3576 · Cited by 222
Self-citationNew approaches for metagenome assembly with short reads
Ayling, M., Clark, M. D., & Leggett, R. M. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bbz020 · Cited by 228
“Theseincludepopular genomic assemblers such as Velvet [14], ABySS [15] and SOAP-denovo [16].”
MethodAhola, V., Lehtonen, R., Somervuo, P. J., Salmela, L., Koskinen, P., Rastas, P. M. A., Välimäki, N., Paulin, L. G., Kvist, J., Wahlberg, N., et al. (2014) · Nature Communications · doi:10.1038/ncomms5737 · Cited by 210
“After scaffolding we used IlluminaPE libraries to close the gaps between the contigs using SOAPdenovo GapCloser 50 .”
Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics
Young, A. D., & Gillung, J. P. (2019) · Systematic Entomology · doi:10.1111/syen.12406 · Cited by 238
“The most commonly used programs for de novo assembly in phy-logenomics include velvet (Zerbino & Birney, 2008), trinity (Grabherr, 2011), soapdenovo (Li et al. , 2010), spades (Banke-vich, 2012) and abyss 2.0 (Jackman et al. , 2017).”
MethodInfluentialKim, K., Lee, S.-C., Lee, J., Yu, Y., Yang, K., Choi, B., Koh, H., Waminal, N. E., Choi, H.-I., Kim, N., et al. (2015) · Scientific Reports · doi:10.1038/srep15655 · Cited by 213
Meraculous: De Novo Genome Assembly with Short Paired-End Reads
Chapman, J., Ho, I., Sunkara, S., Luo, S. J., Schroth, G. P., & Rokhsar, D. S. (2011) · PLoS ONE · doi:10.1371/journal.pone.0023501 · Cited by 221
“[18]) including EULER-SR [19], Velvet [20,21], ALLPATHS [22,23], ABySS [9] and SOAPdenovo [11].”
BackgroundMethodInfluentialWhole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution
Chen, J., Huang, Q., Gao, D., Wang, J., Lang, Y., Li, B., Li, B., Bai, Z., Goicoechea, J. L., Liang, C., et al. (2013) · Nature Communications · doi:10.1038/ncomms2596 · Cited by 214
“The sequence assembly was performed with SOAP denovo 19 .”
Self-citationBuilding near-complete plant genomes
Michael, T. P., & VanBuren, R. (2020) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2019.12.009 · Cited by 212
Hao, D., Ge, G., Xiao, P., Zhang, Y., & Yang, L. (2011) · PLoS ONE · doi:10.1371/journal.pone.0021220 · Cited by 211
“SOAPdenovo firstly combines reads with certain length of overlap to form longer fragments without N, which are called contigs.”
MethodInfluentialOutbred genome sequencing and CRISPR/Cas9 gene editing in butterflies
Li, X., Fan, D., Zhang, W., Liu, G., Zhang, L., Zhao, L., Fang, X., Chen, L., Dong, Y., Chen, Y., et al. (2015) · Nature Communications · doi:10.1038/ncomms9212 · Cited by 209
Self-citationThe genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing
Barrio, Á. M., Lamichhaney, S., Fan, G., Rafati, N., Pettersson, M. E., Zhang, H., Dainat, J., Ekman, D. S., Höppner, M. P., Jern, P., et al. (2016) · eLife · doi:10.7554/elife.12081 · Cited by 212
“04 release 238 (Li et al., 2010) resulted in a scaffolded assembly of 834 Mb (Supplementary file 1B).”
BackgroundMetagenomics methods for the study of plant-associated microbial communities: A review
Fadiji, A. E., & Babalola, O. O. (2020) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2020.105860 · Cited by 228
De novo assembly of short sequence reads
Paszkiewicz, K., & Studholme, D. J. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbq020 · Cited by 204
“20 (13 August 2009) [85, 86] SOPRA 1 (date unknown) [87, 88] SSAKE 3.”
MethodComparative Chloroplast Genomes of Camellia Species
Yang, J., Yang, S., Li, H., Yang, J., & Li, D.-Z. (2013) · PLoS ONE · doi:10.1371/journal.pone.0073053 · Cited by 206
“First, the filtered short reads were assembled into non-redundant contigs using SOAPdenovo [50], a de novo sequence assembly software, with k=31 bp and scaffolding contigs having a minimum size of 100 bp.”
MethodGenome sequences of wild and domestic bactrian camels
Jirimutu, Wang, Z., Ding, G., Chen, G., Sun, Y., Sun, Z., Zhang, H., Wang, L., Hasi, S., Zhang, Y., et al. (2012) · Nature Communications · doi:10.1038/ncomms2192 · Cited by 210
Self-citationZhou, X., Wang, B., Pan, Q., Zhang, J., Kumar, S., Sun, X., Liu, Z., Pan, H., Lin, Y., Liu, G., et al. (2014) · Nature Genetics · doi:10.1038/ng.3137 · Cited by 205
Self-citationReference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis
Sierro, N., Battey, J. N. D., Ouadi, S., Bovet, L., Goepfert, S., Bakaher, N., Peitsch, M. C., & Ivanov, N. V. (2013) · Genome biology · doi:10.1186/gb-2013-14-6-r60 · Cited by 209
“The paired and single reads from the paired-end libraries were then assembled into contigs using SOAPdenovo [81] with a k-mer of 63, and the paired reads from paired-end and mate-pair libraries were used for scaffolding by increasing library size.”
MethodMcCoy, R. C., Taylor, R. W., Blauwkamp, T. A., Kelley, J. L., Kertesz, M., Pushkarev, D., Petrov, D. A., & Fiston-Lavier, A.-S. (2014) · PLoS ONE · doi:10.1371/journal.pone.0106689 · Cited by 206
“In addition to coverage, current approaches to deal with repeats such as TEs generally rely on paired-69 end data (Alkan et al., 2010; Miller et al., 2010; Li et al., 2010).”
MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit
Kultima, J. R., Sunagawa, S., Li, J., Chen, W., Chen, H., Mende, D. R., Arumugam, M., Pan, Q., Liu, B., Qin, J., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0047656 · Cited by 204
“06) of SOAPdenovo [19] is used.”
Self-citationHypervariable loci in the human gut virome
Minot, S. S., Grunberg, S., Wu, G. D., Lewis, J. D., & Bushman, F. D. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1119061109 · Cited by 195
“The raw sequences were assembled into contigs using the deBruijn graph-based assembler SOAPdenovo (10).”
MethodInfluentialAdaptations to a Subterranean Environment and Longevity Revealed by the Analysis of Mole Rat Genomes
Fang, X., Seim, I., Huang, Z., Gerashchenko, M. V., Xiong, Z., Turanov, A. A., Zhu, Y., Lobanov, A. V., Fan, D., Yim, S. H., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.07.030 · Cited by 205
Self-citationSex-Specific Adaptation Drives Early Sex Chromosome Evolution in Drosophila
Zhou, Q., & Bachtrog, D. (2012) · Science · doi:10.1126/science.1225385 · Cited by 200
The present and future ofde novowhole-genome assembly
Sohn, J.-I., & Nam, J. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbw096 · Cited by 213
Chu, B., Petrovich, M. L., Chaudhary, A., Wright, D., Murphy, B. T., Wells, G., & Poretsky, R. S. (2018) · Applied and Environmental Microbiology · doi:10.1128/aem.02168-17 · Cited by 195
“22- m filters combined for assemblies, using a range of k-mers (35 to 63) with a hybrid protocol that combines Velvet (38), SOAPdenovo (39), and Newbler 2.”
Origin of metazoan cadherin diversity and the antiquity of the classical cadherin/β-catenin complex
Nichols, S., Roberts, B., Richter, D. J., Fairclough, S. R., & King, N. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1120685109 · Cited by 195
“For example, classical cadherins are distinguished by the presence of a cytoplasmic cadherin domain (CCD) at the C terminus that regulates interactions with the cytoplasmic protein β-catenin (2, 3, 12, 15).”
BackgroundMethodInfluentialPlastid phylogenomic insights into the evolution of Caryophyllales
Yao, G., Jin, J., Li, H., Yang, J., Mandala, V. S., Croley, M., Mostow, R. S., Douglas, N. A., Chase, M. W., Christenhusz, M. J. M., et al. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.12.023 · Cited by 189
Xia, X., Gurr, G. M., Vasseur, L., Zheng, D., Zhong, H., Qin, B., Lin, J., Wang, Y., Song, F., Li, Y., et al. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00663 · Cited by 189
“For each sample, the effective reads were assembled to obtain long contigs by using SOAP de novo assembler (Li et al., 2010).”
MethodSelf-citationDraft Sequences of the Radish (Raphanus sativus L.) Genome
Kitashiba, H., Feng, L., Hirakawa, H., Kawanabe, T., Zou, Z., Hasegawa, Y., Tonosaki, K., Shirasawa, S., Fukushima, A., Yokoi, S., et al. (2014) · DNA Research · doi:10.1093/dnares/dsu014 · Cited by 188
A hybrid approach for the automated finishing of bacterial genomes
Bashir, A., Klammer, A. A., Robins, W. P., Chin, C.-S., Webster, D. R., Paxinos, E. E., Hsu, D., Ashby, M., Wang, S., Peluso, P. S., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2288 · Cited by 186
“…methods offer substantial computational efficiencies, they have quickly become the preferred computational approach for the de novo assembly of second-generation, short-read data 18–23 , whereas the overlap-layout-consensus approach is the standard for data with lower coverage and longer reads.”
BackgroundZeng, X., Long, H., Wang, Z., Zhao, S., Tang, Y., Huang, Z., Wang, Y., Xu, Q., Mao, L., Deng, G., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1423628112 · Cited by 186
Self-citationClark, S., Egan, R. S., Frazier, P. I., & Wang, Z. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts723 · Cited by 183
“…volumes of sequence data, reference genomes are now rapidly produced using the whole genome shotgun strategy, from small, simple microbial genomes (Wu et al ., 2009) to large, complex plant or mammalian genomes (Fujimoto et al ., 2010; Li et al ., 2010; Schmutz et al. , 2010; Zimin et al. , 2008).”
Impacts of the Three Gorges Dam on microbial structure and potential function
Yan, Q., Bi, Y., Deng, Y., He, Z., Wu, L., Nostrand, J. D. V., Shi, Z. J., Li, J., Wang, X., Hu, Z., et al. (2015) · Scientific Reports · doi:10.1038/srep08605 · Cited by 186
Self-citationCurrent challenges in de novo plant genome sequencing and assembly
Schatz, M. C., WITKOWSKI, J. A., & McCombie, W. R. (2012) · Genome biology · doi:10.1186/gb-2012-13-4-243 · Cited by 184
“Several short-read assembly packages have been proven for mammalian-sized genomes up to the 3 Gbp human genome, including ABySS [51], ALLPATHS-LG [31], the Celera Assembler [52,53], Newbler [54], SGA [55] and SOAPdenovo [56].”
The draft genome of the carcinogenic human liver fluke Clonorchis sinensis
Wang, X., Chen, W., Huang, Y., Sun, J., Men, J., Liu, H., Luo, F., Guo, L., Lv, X., Deng, C., et al. (2011) · Genome biology · doi:10.1186/gb-2011-12-10-r107 · Cited by 183
“sinensis protein sequences against a protein database built from the other eight species (e-value < 1E-10), and the Solar program was used to concatenate fragmentary alignments for each pair of genes [64].”
MethodWenping, H., Zhang, Y., Jie, S., Lijun, Z., & Wang, Z. (2011) · Genomics · doi:10.1016/j.ygeno.2011.03.012 · Cited by 181
Wawrzyn, G. T., Quin, M. B., Choudhary, S., López‐Gallego, F., & Schmidt-Dannert, C. (2012) · Chemistry & Biology · doi:10.1016/j.chembiol.2012.05.012 · Cited by 181
“Paired-end (90 bp reads) Illumina sequencing of a 500 bp fragment library yielded 2,500 Mb of clean data that were assembled into genomic sequences using SOAPdenovo (Li et al., 2010).”
MethodTang, Q., Ma, X., Mo, C., Wilson, I. W., Cai, S., Zhao, H., Yang, Y., Fu, W., & Qiu, D. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-343 · Cited by 180
“The reads obtained were randomly clipped into 21 bp Kmers for assembly using de Bruijn graph and SOAP denovo software [43].”
MethodCannarozzi, G. M., Plaza‐Wüthrich, S., Esfeld, K., Larti, S., Wilson, Y. S., Girma, D., de Castro, E., Chanyalew, S., Blösch, R., Farinelli, L., et al. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-581 · Cited by 187
Chen, X., Bracht, J. R., Goldman, A. D., Dolzhenko, E., Clay, D. M., Swart, E. C., Perlman, D. H., Doak, T. G., Stuart, A. B., Amemiya, C. T., et al. (2014) · Cell · doi:10.1016/j.cell.2014.07.034 · Cited by 186
“(2013) and assembled a transcriptome using only reads that do not map to the MAC genome assembly with SOAPdenovo-Trans (Li et al., 2010), Trinity (Grabherr et al.”
Dugas, D. V., Hernandez, D., Koenen, E. J. M., Schwarz, E. N., Straub, S. C. K., Hughes, C. E., Jansen, R. K., Nageswara‐Rao, M., Staats, M., Trujillo, J. T., et al. (2015) · Scientific Reports · doi:10.1038/srep16958 · Cited by 179
Stull, G. W., Qu, X., Parins‐Fukuchi, C., Yang, Y., Yang, J., Yang, Z.-Y., Hu, Y., Mā, H., Soltis, P. S., Soltis, D. E., et al. (2021) · Nature Plants · doi:10.1038/s41477-021-00964-4 · Cited by 181
The genomic and functional landscapes of developmental plasticity in the American cockroach
Li, S., Zhu, S., Jia, Q., Yuan, D., Ren, C., Li, K., Liu, S., Cui, Y., Zhao, H., Cao, Y., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03281-1 · Cited by 185
Self-citationMicrobial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill
Rodriguez‐R, L. M., Overholt, W. A., Hagan, C., Huettel, M., Kostka, J. E., & Konstantinidis, K. T. (2015) · The ISME Journal · doi:10.1038/ismej.2015.5 · Cited by 177
“Briefly, sequences were assembled with Velvet (Zerbino & Birney, 2008) and SOAP de novo (Li et al., 2010) using k-mer values ranging from 21 to 63.”
MethodRapid diversification of five Oryza AA genomes associated with rice adaptation
Zhang, Q., Zhu, T., Xia, E., Shi, C., Liu, Y.-L., Zhang, Y., Liu, Y., Jiang, W., Zhao, Y., Mao, S., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1418307111 · Cited by 179
“These genomes were assembled using SOAPdenovo (22), resulting in final assembles ranging from 334.7 Mb (GLU) to 375.0 Mb (NIV).”
MethodInfluentialTargeted Next-Generation Sequencing for the Molecular Genetic Diagnostics of Cardiomyopathies
Meder, B., Haas, J., Keller, A., Heid, C., Just, S., Borries, A., Boisguérin, V., Scharfenberger‐Schmeer, M., Stähler, P. F., Beier, M., et al. (2011) · Circulation Cardiovascular Genetics · doi:10.1161/circgenetics.110.958322 · Cited by 178
Correcting errors in short reads by multiple alignments
Salmela, L., & Schröder, J. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr170 · Cited by 176
Yang, H., Huang, X., Fang, S., Xin, W., Huang, L., & Chen, C. (2016) · Scientific Reports · doi:10.1038/srep27427 · Cited by 180
Self-citationGao, C., Wang, Y., Shen, Y., Yan, D., He, X., Dai, J., & Wu, Q. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-582 · Cited by 175
“01 [37]”
Dong, Y., Li, Y., Zhao, M., Jing, M., Liu, X., Liu, M., Guo, X., Zhang, X., Chen, Y., Liu, Y., et al. (2015) · PLoS Pathogens · doi:10.1371/journal.ppat.1004801 · Cited by 181
Self-citationGenome Sequencing and Comparative Genomics of the Broad Host-Range Pathogen Rhizoctonia solani AG8
Hane, J. K., Anderson, J. P., Williams, A., Sperschneider, J., & Singh, K. B. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004281 · Cited by 179
“extension, min size 500 bp) [66] and subject to 5 rounds of Gapcloser2 [65] using paired-end and 39 end merged single-end”
MethodInfluentialGekko japonicus genome reveals evolution of adhesive toe pads and tail regeneration
Liu, Y., Zhou, Q., Wang, Y., Luo, L., Yang, J. M., Yang, L., Liu, M., Li, Y., Qian, T., Zheng, Y., et al. (2015) · Nature Communications · doi:10.1038/ncomms10033 · Cited by 175
“Whole-genome assembly was performed using SOAPdenovo 52 and SSPACE software 53 .”
Self-citationGenetic architecture of colorectal cancer
Peters, U., Bien, S. A., & Zubair, N. (2015) · Gut · doi:10.1136/gutjnl-2013-306705 · Cited by 179
Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios
Besenbacher, S., Liu, S. M., Izarzugaza, J. M. G., Grove, J., Belling, K., Bork‐Jensen, J., Huang, S., Als, T. D., Li, S., Yadav, R., et al. (2015) · Nature Communications · doi:10.1038/ncomms6969 · Cited by 169
Self-citationAcoel genome reveals the regulatory landscape of whole-body regeneration
Gehrke, A. R., Neverett, E. R., Luo, Y., Brandt, A., Ricci, L., Hulett, R. E., Gompers, A. D., Ruby, J. G., Rokhsar, D. S., Reddien, P. W., et al. (2019) · Science · doi:10.1126/science.aau6173 · Cited by 172
“The draft assembly, achieved by the sequential application of SOAPdenovo (15), PRICE (16), SSPACE (17), and the Chicago method (18), totals 950 Mb of sequence (11.8% gaps) (14).”
MethodInfluentialLi, M., Chen, L., Tian, S., Lin, Y., Tang, Q., Zhou, X., Li, D., Yeung, C. K. L., Che, T., Jin, L. G., et al. (2016) · Genome Research · doi:10.1101/gr.207456.116 · Cited by 173
“To identify signatures of diversifying selection of pig breeds, relative homozygous SNP density (RSD) in nonoverlapping 10-kb windows across the reference genome was calculated for each individual using a previously reported methodology (Supplemental Methods; Atanur et al. 2013).”
InfluentialSelf-citationTao, X., Gu, Y.-H., Wang, H.-Y., Zheng, W., Li, X., Zhao, C.-W., & Zhang, Y.-Z. (2012) · PLoS ONE · doi:10.1371/journal.pone.0036234 · Cited by 168
“The results showed that, Velvet produced better assembly result than SOAPdenovo, while Edena generated more short contigs (Table 1).”
MethodInfluentialBowe, A., Onodera, T., Sadakane, K., & Shibuya, T. (2012) · Lecture notes in computer science · doi:10.1007/978-3-642-33122-0_18 · Cited by 171
“Most modern assembler programs use this paradigm [12, 13, 14, 15, 16, 17, 18, 19].”
BackgroundMethodChan, T., Ji, K., Yim, A. K., Liu, X.-Y., Zhou, J.-W., Li, R.-Q., Yang, Y., Li, J., Li, M., Law, P. T. W., et al. (2014) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2014.09.031 · Cited by 170
Self-citationAn overview to the investigative approach to species testing in wildlife forensic science
Linacre, A. M. T., & Tobe, S. S. (2011) · Investigative Genetics · doi:10.1186/2041-2223-2-2 · Cited by 170
“New methods of DNA sequencing open the prospect of sequencing whole genomes [112-114].”
MethodFan, H., Ives, A. R., Surget‐Groba, Y., & Cannon, C. H. (2015) · BMC Genomics · doi:10.1186/s12864-015-1647-5 · Cited by 175
“For the tropical trees, species from the same genus ( Lithocarpus ) were not grouped together, and the relationship between genera within Fagaceae was not consistent with previous studies [41].”
ResultTranscriptomic profiling of the salt-stress response in the wild recretohalophyte Reaumuria trigyna
Dang, Z., Zheng, L., Wang, J., Gao, Z., Wu, S., Qi, Z., & Wang, Y. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-29 · Cited by 169
“Transcriptome de novo assembly was carried out with the short reads assembly program, SOAPdenovo, with the default settings, except that the K-mer value was 25-mer [47].”
MethodSelf-citationLi, Z., Feng, C., Luo, X., Yao, H., Zhang, D., & Zhang, T. (2018) · Food Microbiology · doi:10.1016/j.fm.2018.07.001 · Cited by 169
Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle
Zhan, X., Pan, S., Wang, J., Dixon, A., He, J., Muller, M. G., Ni, P., Hu, L. H., Liu, Y., Hou, H., et al. (2013) · Nature Genetics · doi:10.1038/ng.2588 · Cited by 171
Self-citationYe, L., Zhang, T., Wang, T., & Fang, Z. (2012) · Environmental Science & Technology · doi:10.1021/es303454k · Cited by 168
Reference‐free transcriptome assembly in non‐model animals from next‐generation sequencing data
Cahais, V., Gayral, P., Tsagkogeorga, G., Melo‐Ferreira, J., Ballenghien, M., Weinert, L. A., Chiari, Y., Belkhir, K., Ranwez, V., & Galtier, N. (2012) · Molecular Ecology Resources · doi:10.1111/j.1755-0998.2012.03148.x · Cited by 166
“…Celera (version 6.1, Myers et al. 2000; settings as suggested by O’Neil et al. 2010), Mira (version 3.0.3, Chevreux et al. 2004), Newbler (version 2.6), TransAbyss (Robertson et al. 2010), Soap_de_novo_Trans (version 1.01, Li et al. 2010) and Trinity (version R2011-10-29, Grabherr et al. 2011).”
BackgroundInfluentialFunctional assignment of metagenomic data: challenges and applications
Prakash, T., & Taylor, T. D. (2012) · Briefings in Bioinformatics · doi:10.1093/bib/bbs033 · Cited by 164
“org/forge/ Arachne [5] JAZZ [6] Celera [7] Velvet [8] Newbler 454 Life Sciences SOAPdenovo [9] EULER [10] ORFome assembly [11] IDBA-UD [12] Gene prediction Metagene [13] GeneMark [14] ORF-Finder http://www.”
BackgroundSystems biology-guided biodesign of consolidated lignin conversion
Lin, L., Cheng, Y., Pu, Y., Sun, S., Li, X., Jin, M., Pierson, E. A., Gross, D. C., Dale, B. E., Dai, S. Y., et al. (2016) · Green Chemistry · doi:10.1039/c6gc01131d · Cited by 164
Pan, G., Xu, J., Li, T., Xia, Q., Liu, S., Zhang, G., Li, S., Li, C., Liu, H., Yang, L., et al. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-186 · Cited by 167
“bombycis genome, the illumina reads were assembled by BGI’s de novo assembly software [42], which assembled unique and frequency repeat areas of genome.”
MethodSelf-citationThe resurrection genome of Boea hygrometrica : A blueprint for survival of dehydration
Xiao, L., Ge, Y., Zhang, L., Yang, X., Zhao, S., Ji, Z., Zhou, Q., Hu, M., Wang, Y., Chen, M., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1505811112 · Cited by 168
“Resurrection plants offer a potential source of genes for improvement of crop drought tolerance (5, 6) as the demand for fresh water grows (7).”
BackgroundMethodInfluential
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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