The DOI matches its Crossref record; 23 of the 23 references it cites were found in a registry or an index.
TransRate: reference-free quality assessment of de novo transcriptome assemblies
Open accessAbstract
TransRate is a tool for reference-free quality assessment of de novo transcriptome assemblies. Using only the sequenced reads and the assembly as input, we show that multiple common artifacts of de novo transcriptome assembly can be readily detected. These include chimeras, structural errors, incomplete assembly, and base errors. TransRate evaluates these errors to produce a diagnostic quality score for each contig, and these contig scores are integrated to evaluate whole assemblies. Thus, TransRate can be used for de novo assembly filtering and optimization as well as comparison of assemblies generated using different methods from the same input reads. Applying the method to a data set of 155 published de novo transcriptome assemblies, we deconstruct the contribution that assembly method, read length, read quantity, and read quality make to the accuracy of de novo transcriptome assemblies and reveal that variance in the quality of the input data explains 43% of the variance in the quality of published de novo transcriptome assemblies. Because TransRate is reference-free, it is suitable for assessment of assemblies of all types of RNA, including assemblies of long noncoding RNA, rRNA, mRNA, and mixed RNA samples.
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Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes
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Genomic signatures associated with transitions to viviparity in cyprinodontiformes
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Metadata
- Authors
- Smith-Unna, R., Boursnell, C., Patro, R., Hibberd, J. M., & Kelly, S.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2016-06-01
- Volume
- 26
- Issue
- 8
- Pages
- 1134-1144
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- OpenAlex
- W2409002067
- Cited by
- 837
- References
- 23
- Type
- posted content
- Language
- en
- Open access
- bronze
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- Smith-Unna, R., Boursnell, C., Patro, R., Hibberd, J. M., & Kelly, S. (2016). TransRate: reference-free quality assessment of de novo transcriptome assemblies. Genome Research. https://doi.org/10.1101/gr.196469.115
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