This is the Windows app named CStone whose latest release can be downloaded as cstone.zip. It can be run online in the free hosting provider OnWorks for workstations.
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CStone is a de novo assembler for RNA-Seq data that uses de Bruijn like graphs and annotates each contig produced with one of three graph classification levels indicating whether or not it can be guaranteed to be non chimeric. Classification levels are dependent on the complexity of the gene family from which the reads are derived. As a by-product, this also provides insight into the structural makeup of the underlying gene families that have been sequenced. It has been tested on both simulated and real data and benchmarked against two widely established de novo assemblers Trinity and rnaSPAdes. Further details will be available shortly within our paper.
The Portuguese Foundation for Science and Technology, FCT, supported this work through project PTDC/BIA-EVL/29115/2017. John Archer and Raquel Linheiro were supported by Funds under the reference POCI-01-0145-FEDER-029115.
- De novo assembly of RNA-Seq data.
- Identification of non-chimeric contigs.
- Cross-platform compatibility.
- Executable jar available.
- No external packages required.
- Code easy to follow and incorporated to other tools.
- Information on complexity of underlying gene families.
- de Bruijn like (more lenient) approach.
This is an application that can also be fetched from https://sourceforge.net/projects/cstone/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.