The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Assembly algorithms for next-generation sequencing data
Open accessAbstract
The emergence of next-generation sequencing platforms led to resurgence of research in whole-genome shotgun assembly algorithms and software. DNA sequencing data from the Roche 454, Illumina/Solexa, and ABI SOLiD platforms typically present shorter read lengths, higher coverage, and different error profiles compared with Sanger sequencing data. Since 2005, several assembly software packages have been created or revised specifically for de novo assembly of next-generation sequencing data. This review summarizes and compares the published descriptions of packages named SSAKE, SHARCGS, VCAKE, Newbler, Celera Assembler, Euler, Velvet, ABySS, AllPaths, and SOAPdenovo. More generally, it compares the two standard methods known as the de Bruijn graph approach and the overlap/layout/consensus approach to assembly.
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Cites
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
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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-citationBase-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439
SOAP: Short oligonucleotide alignment program
Li, R., Li, Y., Kristiansen, K., & Wang, J. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn025 · Cited by 3,597
De novo assembly of human genomes with massively parallel short read sequencing
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“The SOAPdenovo program [59] generated high-quality mammalian genome sequences from billions of Solexa reads of length 75 bp and less [60,61].”
The sequence and de novo assembly of the giant panda genome
Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., Huang, Q., Cai, Q., Li, B., Bai, Y., et al. (2010) · Nature · doi:10.1038/nature08696 · Cited by 1,180
The fragment assembly string graph
Myers, E. W. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti1114 · Cited by 424
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The human gut virome: inter-individual variation and dynamic response to diet
Minot, S., Sinha, R., Chen, J., Li, H., Keilbaugh, S. A., Wu, G. D., Lewis, J. D., & Bushman, F. D. (2011) · Genome Research · doi:10.1101/gr.122705.111 · Cited by 935
The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line
Xu, X., Nagarajan, H., Lewis, N. E., Pan, S., Cai, Z., Liu, X., Chen, W., Xie, M., Wang, W., Hammond, S., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1932 · Cited by 785
The genome sequence of Atlantic cod reveals a unique immune system
Star, B., Nederbragt, A. J., Jentoft, S., Grimholt, U., Malmstrøm, M., Gregers, T. F., Rounge, T. B., Paulsen, J., Solbakken, M. H., Sharma, A., et al. (2011) · Nature · doi:10.1038/nature10342 · Cited by 741
How to apply de Bruijn graphs to genome assembly
Compeau, P. E. C., Pevzner, P. A., & Tesler, G. (2011) · Nature Biotechnology · doi:10.1038/nbt.2023 · Cited by 673
Salmonella Serotype Determination Utilizing High-Throughput Genome Sequencing Data
Zhang, S., Yin, Y., Jones, M. B., Zhang, Z., Deatherage Kaiser, B. L., Dinsmore, B. A., Fitzgerald, C., Fields, P. I., & Deng, X. (2015) · Journal of Clinical Microbiology · doi:10.1128/jcm.00323-15 · Cited by 423
Metadata
- Authors
- Miller, J. R., Koren, S., & Sutton, G.
- Venue
- Genomics
- Publisher
- Elsevier BV
- Published
- 2010-06
- Volume
- 95
- Issue
- 6
- Pages
- 315-327
- ISSN
- 0888-7543 (ISSN-L)
- OpenAlex
- W1972924519
- Cited by
- 1,154
- References
- 7
- FWCI
- 38.04
- Type
- journal article
- Language
- en
- Open access
- bronze
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