The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2
Open accessAbstract
We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program, allowing for assembly of mammalian-size genomes, and also improving the assembly of smaller genomes. Three principal changes were simultaneously made and applied to the assembly of the mouse genome, during a six-month period of development: (1) Supercontigs (scaffolds) were iteratively broken and rejoined using several criteria, yielding a 64-fold increase in length (N50), and apparent elimination of all global misjoins; (2) gaps between contigs in supercontigs were filled (partially or completely) by insertion of reads, as suggested by pairing within the supercontig, increasing the N50 contig length by 50%; (3) memory usage was reduced fourfold. The outcome of this mouse assembly and its analysis are described in (Mouse Genome Sequencing Consortium 2002).
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Cites
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
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
Mullikin, J. C., & Ning, Z. (2003) · Genome Research · doi:10.1101/gr.731003 · Cited by 222
Cited by
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
A fast, lock-free approach for efficient parallel counting of occurrences of k -mers
Marçais, G., & Kingsford, C. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr011 · Cited by 4,661
Genome sequence, comparative analysis and haplotype structure of the domestic dog
members, B. S. P., Lindblad-Toh, K., Wade, C. M., Mikkelsen, T. S., Karlsson, E. K., Jaffe, D. B., Kamal, M., Clamp, M., Chang, J. L., Kulbokas, E. J., et al. (2005) · Nature · doi:10.1038/nature04338 · Cited by 2,568
Self-citationInitial sequence of the chimpanzee genome and comparison with the human genome
The Chimpanzee Sequencing and Analysis Consortium (2005) · Nature · doi:10.1038/nature04072 · Cited by 2,459
Jaillon, O., Aury, J.-M., Brunet, F., Petit, J.-L., Stange-Thomann, N., Mauceli, E., Bouneau, L., Fischer, C., Ozouf-Costaz, C., Bernot, A., et al. (2004) · Nature · doi:10.1038/nature03025 · Cited by 1,966
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Metadata
- Authors
- Jaffe, D. B., Butler, J., Gnerre, S., Mauceli, E., Lindblad-Toh, K., Mesirov, J. P., Zody, M. C., & Lander, E. S.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2003-01-01
- Volume
- 13
- Issue
- 1
- Pages
- 91-96
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- OpenAlex
- W1992950355
- Cited by
- 307
- References
- 3
- Type
- posted content
- Language
- en
- Open access
- bronze
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- Jaffe, D. B., Butler, J., Gnerre, S., Mauceli, E., Lindblad-Toh, K., Mesirov, J. P., Zody, M. C., & Lander, E. S. (2003). Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2. Genome Research. https://doi.org/10.1101/gr.828403
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