The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Minimus: a fast, lightweight genome assembler
Open accessAbstract
Background: Genome assemblers have grown very large and complex in response to the need for algorithms to handle the challenges of large whole-genome sequencing projects. Many of the most common uses of assemblers, however, are best served by a simpler type of assembler that requires fewer software components, uses less memory, and is far easier to install and run. Results: We have developed the Minimus assembler to address these issues, and tested it on a range of assembly problems. We show that Minimus performs well on several small assembly tasks, including the assembly of viral genomes, individual genes, and BAC clones. In addition, we evaluate Minimus' performance in assembling bacterial genomes in order to assess its suitability as a component of a larger assembly pipeline. We show that, unlike other software currently used for these tasks, Minimus produces significantly fewer assembly errors, at the cost of generating a more fragmented assembly. Conclusion: We find that for small genomes and other small assembly tasks, Minimus is faster and far more flexible than existing tools. Due to its small size and modular design Minimus is perfectly suited to be a component of complex assembly pipelines. Minimus is released as an open-source software project and the code is available as part of the AMOS project at Sourceforge.
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Cites
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
Base-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
CAP3: A DNA Sequence Assembly Program
Huang, X., & Madan, A. (1999) · Genome Research · doi:10.1101/gr.9.9.868 · Cited by 5,261
Reducing storage requirements for biological sequence comparison
Roberts, M., Hayes, W., Hunt, B. R., Mount, S. M., & Yorke, J. A. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth408 · Cited by 485 · cited 1×
“hash-overlap – a sequence overlapper that uses minimizers [27] to increase speed and decrease memory usage.”
BackgroundMullikin, J. C., & Ning, Z. (2003) · Genome Research · doi:10.1101/gr.731003 · Cited by 222
Cited by
Vieler, A., Wu, G., Tsai, C.-H., Bullard, B., Cornish, A. J., Harvey, C., Reca, I.-B., Thornburg, C., Achawanantakun, R., Buehl, C. J., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1003064 · Cited by 458
Naccache, S. N., Federman, S., Veeraraghavan, N., Zaharia, M., Lee, D., Samayoa, E., Bouquet, J., Greninger, A. L., Luk, K.-C., Enge, B., et al. (2014) · Genome Research · doi:10.1101/gr.171934.113 · Cited by 460
Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease
Liu, B., Faller, L. L., Klitgord, N., Mazumdar, V., Ghodsi, M., Sommer, D. D., Gibbons, T. R., Treangen, T. J., Chang, Y.-C., Li, S., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037919 · Cited by 411
Self-citationDe novo assembly of short sequence reads
Paszkiewicz, K., & Studholme, D. J. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbq020 · Cited by 204
Defining the Origins of the NOD-Like Receptor System at the Base of Animal Evolution
Lange, C., Hemmrich, G., Klostermeier, U. C., Lopez-Quintero, J. A., Miller, D. J., Rahn, T., Weiss, Y., Bosch, T. C. G., & Rosenstiel, P. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msq349 · Cited by 150
Metadata
- Authors
- Sommer, D. D., Delcher, A. L., Salzberg, S. L., & Pop, M.
- Venue
- BMC Bioinformatics
- Published
- 2007-02-26
- Volume
- 8
- Issue
- 1
- Pages
- 64-64
- ISSN
- 1471-2105 (ISSN-L)
- OpenAlex
- W2033531015
- Cited by
- 398
- References
- 5
- FWCI
- 3.71
- Type
- journal article
- Language
- en
- Open access
- gold
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