The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
PCAP: A Whole-Genome Assembly Program
Open accessAbstract
We describe a whole-genome assembly program named PCAP for processing tens of millions of reads. The PCAP program has several features to address efficiency and accuracy issues in assembly. Multiple processors are used to perform most time-consuming computations in assembly. A more sensitive method is used to avoid missing overlaps caused by sequencing errors. Repetitive regions of reads are detected on the basis of many overlaps with other reads, instead of many shorter word matches with other reads. Contaminated end regions of reads are identified and removed. Generation of a consensus sequence for a contig is based on an alignment of reads in the contig, in which both base quality values and coverage information are used to determine every consensus base. The PCAP program was tested on a mouse whole-genome data set of 30 million reads and a human Chromosome 20 data set of 1.7 million reads. The program is freely available for academic use.
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Citations
Cites
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
CAP3: A DNA Sequence Assembly Program
Huang, X., & Madan, A. (1999) · Genome Research · doi:10.1101/gr.9.9.868 · Cited by 5,261
Self-citationMullikin, J. C., & Ning, Z. (2003) · Genome Research · doi:10.1101/gr.731003 · Cited by 222
Cited by
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
“Several programs, such as phrap (http://www.phrap.org), Celera assembler (Myers et al. 2000), ARACHNE (Batzoglou et al. 2002), Phusion (Mullikin and Ning 2003), RePS (Wang et al. 2002), PCAP (Huang et al. 2003), and Atlas (Havlak et al. 2004), have been successfully used for de novo assembly of whole-genome shotgun (W…”
MethodSelf-citationInternational Chicken Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03154 · Cited by 2,750
Initial 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
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
Kurokawa, K., Itoh, T., Kuwahara, T., Oshima, K., Toh, H., Toyoda, A., Takami, H., Morita, H., Sharma, V. K., Srivastava, T. P., et al. (2007) · DNA Research · doi:10.1093/dnares/dsm018 · Cited by 869
A Catalog of Reference Genomes from the Human Microbiome
The Human Microbiome Jumpstart Reference Strains Consortium, Nelson, K. E., Weinstock, G. M., Highlander, S. K., Worley, K. C., Creasy, H. H., Wortman, J. R., Rusch, D. B., Mitreva, M., Sodergren, E., et al. (2010) · Science · doi:10.1126/science.1183605 · Cited by 702
Metadata
- Authors
- Huang, X., Wang, J., Aluru, S., Yang, S.-P., & Hillier, L.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2003-09
- Volume
- 13
- Issue
- 9
- Pages
- 2164-2170
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2141217788
- Cited by
- 288
- References
- 3
- Type
- posted content
- Language
- en
- Open access
- bronze
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