The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
Open accessAbstract
Background: There is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accurate. SOAPdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions. Findings: To overcome these challenges, we have developed its successor, SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome. Conclusions: Benchmark using the Assemblathon1 and GAGE datasets showed that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo and is competitive to other assemblers on both assembly length and accuracy. We also provide an updated assembly version of the 2008 Asian (YH) genome using SOAPdenovo2. Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp, respectively, which is 3-fold and 50-fold longer than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 lower during the point of largest memory consumption.
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Citations
Cites
De novo assembly of human genomes with massively parallel short read sequencing
Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., et al. (2010) · Genome Research · doi:10.1101/gr.097261.109 · Cited by 2,926 · cited 4×
“The previous assembly was done using SOAPdenovo1 [3], but in addition it was also limited by the very short read lengths (~35 bp) that were the standard output of Illumina Genome Analyzers (GAIIx) at that time and by the insert sizes available (maximum size is 10 kb).”
BackgroundMethodInfluentialSelf-citationThe diploid genome sequence of an Asian individual
Wang, J., Wang, W., Li, R., Li, Y., Tian, G., Goodman, L., Fan, W., Zhang, J., Li, J., Zhang, J., et al. (2008) · Nature · doi:10.1038/nature07484 · Cited by 924 · cited 1×
“We also used SOAPdenovo2 to reassemble and update the previously assembled YH Asian Genome [12].”
MethodSelf-citation
Research works printed but not linked: 15
- Earl, 2011, Assemblathon 1: a competitive assessment of de novo short read assembly methods, Genome Res, 21, 2224, 10.1101/gr.126599.111 · DOI · Paper page
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- The Assemblathon.
- Wang J, Li Y, Luo R, Liu B, Xie Y, Li Z, Fang X, Zheng H, Qin J, Yang B, Yu C, Ni P, Li N, Guo G, Ye J, Fang L, Su Y, Asan , Zheng H, Kristiansen K, Wong GK, Nielsen R, Durbin R, Bolund L, Zhang X, Li S, Yang H, Wang J. 2012, Updated genome assembly of YH: the first diploid genome sequence of a Han Chinese individual (version 2, 07/2012), GigaScience Database, 10.5524/100038. · doi:10.5524/100038
- The UCSC Genome Bioinformatics site.
- She, 2004, Shotgun sequence assembly and recent segmental duplications within the human genome, Nature, 431, 927, 10.1038/nature03062 · DOI · Paper page
- Yan Huang - The first Asian diploid genome.
- Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung D, Yiu SM, Liu G, Zhu X, Peng S, Li Y, Yang H, Wang J, Lam TW, Wang J. 2012, Software and supporting material for “SOAPdenovo2: an empirically improved memory-efficient short read de novo assembly”, GigaScience Database, 10.5524/100044. · doi:10.5524/100044
Cited by
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
Kim, D., Paggi, J. M., Park, C., Bennett, C., & Salzberg, S. L. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0201-4 · Cited by 15,022
Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life
Bäckhed, F., Roswall, J., Peng, Y., Feng, Q., Jia, H., Kovatcheva-Datchary, P., Li, Y., Xia, Y., Xie, H., Zhong, H., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.04.004 · Cited by 3,315
Self-citationTowards complete and error-free genome assemblies of all vertebrate species
Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Kim, J., et al. (2021) · Nature · doi:10.1038/s41586-021-03451-0 · Cited by 3,097
Towards complete and error-free genome assemblies of all vertebrate species
Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Gedman, G. L., et al. (2020) · doi:10.1101/2020.05.22.110833 · Cited by 3,097
Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis
Scher, J. U., Sczesnak, A., Longman, R. S., Segata, N., Ubeda, C., Bielski, C., Rostron, T., Cerundolo, V., Pamer, E. G., Abramson, S. B., et al. (2013) · eLife · doi:10.7554/elife.01202 · Cited by 2,047
Metadata
- Authors
- Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., Liu, Y., Tang, J., Wu, G., Zhang, H., Shi, Y., Liu, Y., Yu, C., Wang, B., Lu, Y., Han, C., Cheung, D. W., Yiu, S.-M., Peng, S., Xiaoqian, Z., Liu, G., Liao, X., Li, Y., Yang, H., Wang, J., Lam, T.-W., & Wang, J.
- Venue
- Gigascience
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-12-01
- Volume
- 1
- Issue
- 1
- Pages
- 18-18
- ISSN
- 2047-217X (ISSN-L)
- OpenAlex
- W2129933858
- Cited by
- 5,307
- References
- 2
- FWCI
- 69.01
- Type
- journal article
- Language
- en
- Update notices
- correction (2015-07-08)
- Open access
- gold
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- Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., Liu, Y., Tang, J., Wu, G., Zhang, H., Shi, Y., Liu, Y., Yu, C., Wang, B., Lu, Y., Han, C., . . . Wang, J. (2012). SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience. https://doi.org/10.1186/2047-217x-1-18
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