The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
Open accessAbstract
Motivation: Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining a large number of gene sequences from an organism with no reference genome. Owing to the rapid increase in throughputs and decrease in costs of next- generation sequencing, RNA-Seq in particular has become the method of choice. However, the very short reads (e.g. 2 × 90 bp paired ends) from next generation sequencing makes de novo assembly to recover complete or full-length transcript sequences an algorithmic challenge. Results: Here, we present SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse. Using as our benchmarks the known transcripts from these well-annotated genomes (sequenced a decade ago), we assessed how SOAPdenovo-Trans and two other popular transcriptome assemblers handled such practical issues as alternative splicing and variable expression levels. Our conclusion is that SOAPdenovo-Trans provides higher contiguity, lower redundancy and faster execution. Availability and implementation: Source code and user manual are available at http://sourceforge.net/projects/soapdenovotrans/. Contact: xieyl@genomics.cn or bgi-soap@googlegroups.com Supplementary information: Supplementary data are available at Bioinformatics online.
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Phylogenomics resolves the timing and pattern of insect evolution
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Self-citationEvolutionary History of the Hymenoptera
Peters, R. S., Krogmann, L., Mayer, C., Donath, A., Gunkel, S., Meusemann, K., Kozlov, A., Podsiadlowski, L., Petersen, M., Lanfear, R., et al. (2017) · Current Biology · doi:10.1016/j.cub.2017.01.027 · Cited by 894
Self-citationTransRate: reference-free quality assessment of de novo transcriptome assemblies
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Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations
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Metadata
- Authors
- Xie, Y., Wu, G., Tang, J., Luo, R., Patterson, J., Liu, S., Huang, W., He, G., Gu, S., Li, S., Zhou, X., Lam, T.-W., Li, Y., Xu, X., Wong, G. K.-S., & Wang, J.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-02-13
- Volume
- 30
- Issue
- 12
- Pages
- 1660-1666
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2110392562
- Cited by
- 983
- References
- 7
- FWCI
- 35.04
- Type
- journal article
- Language
- en
- Open access
- green
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- Xie, Y., Wu, G., Tang, J., Luo, R., Patterson, J., Liu, S., Huang, W., He, G., Gu, S., Li, S., Zhou, X., Lam, T.-W., Li, Y., Xu, X., Wong, G. K.-S., & Wang, J. (2014). SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics. https://doi.org/10.1093/bioinformatics/btu077
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