SOAPdenovo-Trans is de novo RNA-seq full-length transcriptome assembler. The SOAPdenovo-Trans algorithm adapts the SOAPdenovo framework, uses the Trinity error removal technique, the graph traversal model from Oases, and uses a transitive reduction to simplify scaffolding graphs. It can handle paired-end reads and multiple insert sizes. The physical memory requirement is large.
Transcriptomics; Gene expression; Gene transcripts
Xie Y, Wu G, Tang J, Luo R, Patterson J, Liu S, Huang W, He G, Gu S, Li S, Zhou X, Lam TW, Li Y, Xu X, Wong GK, Wang J "SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads." Bioinformatics. 2014 Jun 15;30(12):1660-6. Epub 2014 Feb 13. https://doi.org/10.1093/bioinformatics/btu077
PMID: 24532719
If you find errors, please report here.
SECTIONS
TutorialsFind thousands of Bioinformatics and Life Science software tools and databases in the newly launched
Ads