The DOI matches its Crossref record; 40 of the 40 references it cites were found in a registry or an index.
rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data
Open accessAbstract
Background: The possibility of generating large RNA-sequencing datasets has led to development of various reference-based and de novo transcriptome assemblers with their own strengths and limitations. While reference-based tools are widely used in various transcriptomic studies, their application is limited to the organisms with finished and well-annotated genomes. De novo transcriptome reconstruction from short reads remains an open challenging problem, which is complicated by the varying expression levels across different genes, alternative splicing, and paralogous genes. Results: Herein we describe the novel transcriptome assembler rnaSPAdes, which has been developed on top of the SPAdes genome assembler and explores computational parallels between assembly of transcriptomes and single-cell genomes. We also present quality assessment reports for rnaSPAdes assemblies, compare it with modern transcriptome assembly tools using several evaluation approaches on various RNA-sequencing datasets, and briefly highlight strong and weak points of different assemblers. Conclusions: Based on the performed comparison between different assembly methods, we infer that it is not possible to detect the absolute leader according to all quality metrics and all used datasets. However, rnaSPAdes typically outperforms other assemblers by such important property as the number of assembled genes and isoforms, and at the same time has higher accuracy statistics on average comparing to the closest competitors.
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Cites
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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
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Cited by
Using SPAdes De Novo Assembler
Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A., & Korobeynikov, A. (2020) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.102 · Cited by 3,555
Self-citationWildfire-dependent changes in soil microbiome diversity and function
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Viroid-like colonists of human microbiomes
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Viroid-like colonists of human microbiomes
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Transcriptome-wide analysis of differential expression in perturbation atlases
Nadig, A., Replogle, J. M., Pogson, A. N., Murthy, M., McCarroll, S. A., Weissman, J. S., Robinson, E. B., & O’Connor, L. J. (2025) · Nature Genetics · doi:10.1038/s41588-025-02169-3 · Cited by 70
Metadata
- Authors
- Bushmanova, E., Antipov, D., Lapidus, A., & Prjibelski, A. D.
- Venue
- GigaScience
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-09-01
- Volume
- 8
- Issue
- 9
- ISSN
- 2047-217X (ISSN-L)
- OpenAlex
- W2972131171
- Cited by
- 869
- References
- 40
- FWCI
- 22.84
- Type
- journal article
- Language
- en
- Open access
- gold
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