The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Oases:robust de novo RNA-seq assembly across the dynamic range of expression levels
Open accessAbstract
Motivation: High-throughput sequencing has made the analysis of new model organisms more affordable. Although assembling a new genome can still be costly and difficult, it is possible to use RNA-seq to sequence mRNA. In the absence of a known genome, it is necessary to assemble these sequences de novo, taking into account possible alternative isoforms and the dynamic range of expression values. Results: We present a software package named Oases designed to heuristically assemble RNA-seq reads in the absence of a reference genome, across a broad spectrum of expression values and in presence of alternative isoforms. It achieves this by using an array of hash lengths, a dynamic filtering of noise, a robust resolution of alternative splicing events and the efficient merging of multiple assemblies. It was tested on human and mouse RNA-seq data and is shown to improve significantly on the transABySS and Trinity de novo transcriptome assemblers. Availability and implementation: Oases is freely available under the GPL license at www.ebi.ac.uk/~zerbino/oases/ Contact: dzerbino@ucsc.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696
RNA-Seq: a revolutionary tool for transcriptomics
Wang, Z., Gerstein, M., & Snyder, M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2484 · Cited by 13,174
<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
Alternative isoform regulation in human tissue transcriptomes
Wang, E. T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S. F., Schroth, G. P., & Burge, C. B. (2008) · Nature · doi:10.1038/nature07509 · Cited by 5,181
Guttman, M., Garber, M., Levin, J. Z., Donaghey, J., Robinson, J., Adiconis, X., Fan, L., Koziol, M. J., Gnirke, A., Nusbaum, C., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1633 · Cited by 1,253
Optimization of de novo transcriptome assembly from next-generation sequencing data
Surget-Groba, Y., & Montoya-Burgos, J. I. (2010) · Genome Research · doi:10.1101/gr.103846.109 · Cited by 339
Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes
Blencowe, B. J., Ahmad, S., & Lee, L. J. (2009) · Genes & Development · doi:10.1101/gad.1788009 · Cited by 168
Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads
Martin, J., Bruno, V. M., Fang, Z., Meng, X., Blow, M., Zhang, T., Sherlock, G., Snyder, M., & Wang, Z. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-663
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A survey of best practices for RNA-seq data analysis
Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., McPherson, A., Szcześniak, M. W., Gaffney, D. J., Elo, L. L., Zhang, X., et al. (2016) · Genome Biology · doi:10.1186/s13059-016-0881-8 · Cited by 2,794
Kukurba, K. R., & Montgomery, S. B. (2015) · Cold Spring Harbor Protocols · doi:10.1101/pdb.top084970 · Cited by 924
TransRate: reference-free quality assessment of de novo transcriptome assemblies
Smith-Unna, R., Boursnell, C., Patro, R., Hibberd, J. M., & Kelly, S. (2016) · Genome Research · doi:10.1101/gr.196469.115 · Cited by 837
Assessment of transcript reconstruction methods for RNA-seq
The RGASP Consortium, Steijger, T., Abril, J. F., Engström, P. G., Kokocinski, F., Hubbard, T. J., Guigó, R., Harrow, J., & Bertone, P. (2013) · Nature Methods · doi:10.1038/nmeth.2714 · Cited by 699
Haas, B. J., Dobin, A., Li, B., Stransky, N., Pochet, N., & Regev, A. (2019) · Genome biology · doi:10.1186/s13059-019-1842-9 · Cited by 646
Metadata
- Authors
- Schulz, M. H., Zerbino, D. R., Vingron, M., & Birney, E.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-02-24
- Volume
- 28
- Issue
- 8
- Pages
- 1086-1092
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2156841387
- Cited by
- 1,424
- References
- 9
- FWCI
- 60.87
- Type
- journal article
- Language
- en
- Open access
- hybrid
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