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De novo assembly of bacterial transcriptomes from RNA-seq data
Open accessAbstract
Transcriptome assays are increasingly being performed by high-throughput RNA sequencing (RNA-seq). For organisms whose genomes have not been sequenced and annotated, transcriptomes must be assembled de novo from the RNA-seq data. Here, we present novel algorithms, specific to bacterial gene structures and transcriptomes, for analysis of bacterial RNA-seq data and de novo transcriptome assembly. The algorithms are implemented in an open source software system called Rockhopper 2. We find that Rockhopper 2 outperforms other de novo transcriptome assemblers and offers accurate and efficient analysis of bacterial RNA-seq data. Rockhopper 2 is available at http://cs.wellesley.edu/~btjaden/Rockhopper.
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Roles of IFN-γ in tumor progression and regression: A review
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Improving genetic diagnosis in Mendelian disease with transcriptome sequencing
Cummings, B. B., Marshall, J. L., Tukiainen, T., Lek, M., Donkervoort, S., Foley, A. R., Bolduc, V., Waddell, L. B., Sandaradura, S. A., O’Grady, G. L., et al. (2017) · Science Translational Medicine · doi:10.1126/scitranslmed.aal5209 · Cited by 831
A general and flexible method for signal extraction from single-cell RNA-seq data
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DeepCRISPR: Optimized CRISPR guide RNA design by deep learning
Chuai, G., Ma, H., Yan, J., Chen, M., Hong, N., Xue, D., Zhou, C., Zhu, C., Chen, K., Duan, B., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1459-4 · Cited by 641
Metadata
- Authors
- Tjaden, B.
- Venue
- Genome Biology
- Published
- 2015-01-13
- Volume
- 16
- Issue
- 1
- Pages
- 1-1
- ISSN
- 1465-6906 (ISSN-L)
- OpenAlex
- W2154598603
- Cited by
- 1,717
- References
- 10
- FWCI
- 60.72
- Type
- journal article
- Language
- en
- Open access
- gold
- Licence
- creativecommons.org/licenses/by/4.0 (tdm)
- creativecommons.org/licenses/by/4.0 (vor)
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