The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
PRICE: Software for the Targeted Assembly of Components of (Meta) Genomic Sequence Data
Open accessAbstract
Low-cost DNA sequencing technologies have expanded the role for direct nucleic acid sequencing in the analysis of genomes, transcriptomes, and the metagenomes of whole ecosystems. Human and machine comprehension of such large datasets can be simplified via synthesis of sequence fragments into long, contiguous blocks of sequence (contigs), but most of the progress in the field of assembly has focused on genomes in isolation rather than metagenomes. Here, we present software for paired-read iterative contig extension (PRICE), a strategy for focused assembly of particular nucleic acid species using complex metagenomic data as input. We describe the assembly strategy implemented by PRICE and provide examples of its application to the sequence of particular genes, transcripts, and virus genomes from complex multicomponent datasets, including an assembly of the BCBL-1 strain of Kaposi’s sarcoma-associated herpesvirus. PRICE is open-source and available for free download (derisilab.ucsf.edu/software/price/ or sourceforge.net/projects/pricedenovo/).
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Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
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
Genomic Islands in Pathogenic and Environmental Microorganisms
Dobrindt, U., Hochhut, B., Hentschel, U., & Hacker, J. (2004) · Nature Reviews Microbiology · doi:10.1038/nrmicro884 · Cited by 1,188
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
A survey of sequence alignment algorithms for next-generation sequencing
Li, H., & Homer, N. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbq015 · Cited by 875
Biases in Illumina transcriptome sequencing caused by random hexamer priming
Hansen, K. D., Brenner, S. E., & Dudoit, S. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq224 · Cited by 713
Cited by
Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection
Gu, W., Miller, S., & Chiu, C. Y. (2019) · Annual Review of Pathology: Mechanisms of Disease · doi:10.1146/annurev-pathmechdis-012418-012751 · Cited by 1,458
Langelier, C., Kalantar, K. L., Moazed, F., Wilson, M. R., Crawford, E. D., Deiss, T., Belzer, A., Bolourchi, S., Caldera, S., Fung, M., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1809700115 · Cited by 411
Self-citationKalantar, K. L., Carvalho, T., de Bourcy, C. F. A., Dimitrov, B., Dingle, G., Egger, R., Han, J., Holmes, O. B., Juan, Y.-F., King, R., et al. (2020) · GigaScience · doi:10.1093/gigascience/giaa111 · Cited by 406
Self-citationHigh throughput sequencing methods and analysis for microbiome research
Di Bella, J. M., Bao, Y., Gloor, G. B., Burton, J. P., & Reid, G. (2013) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2013.08.011 · Cited by 324
Jeraldo, P., Hernandez, A., Nielsen, H. B., Chen, X., White, B. A., Goldenfeld, N., Nelson, H., Alhquist, D., Boardman, L., & Chia, N. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00783 · Cited by 38
Metadata
- Authors
- Ruby, J. G., Bellare, P., & DeRisi, J. L.
- Venue
- G3 Genes|Genomes|Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-05-01
- Volume
- 3
- Issue
- 5
- Pages
- 865-880
- ISSN
- 2160-1836 (ISSN-L)
- OpenAlex
- W2124648649
- Cited by
- 290
- References
- 7
- FWCI
- 12.24
- Type
- journal article
- Language
- en
- Open access
- gold
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- Ruby, J. G., Bellare, P., & DeRisi, J. L. (2013). PRICE: Software for the Targeted Assembly of Components of (Meta) Genomic Sequence Data. G3 Genes|Genomes|Genetics. https://doi.org/10.1534/g3.113.005967
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