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CStone Summary
CStone is a de novo assembler that utilizes a classification system to label contigs in a manner that indicates whether or not they are non-chimeric. This encourages contig dependent results to be presented with increased objectivity by maintaining the context of ambiguity associated with the assembly process.

Publication

1. Linheiro R, Archer J. CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure. PLOS Comput Biol. 2021;17: e1009631. view

Abstract
With the exponential growth of sequence information stored over the last decade, including that of de novo assembled contigs from RNA-Seq experiments, quantification of chimeric sequences has become essential when assembling read data. In transcriptomics, de novo assembled chimeras can closely resemble underlying transcripts, but patterns such as those seen between co-evolving sites, or mapped read counts, become obscured. We have created a de Bruijn based de novo assembler for RNA-Seq data that utilizes a classification system to describe the complexity of underlying graphs from which contigs are created. Each contig is labelled with one of three levels, indicating whether or not ambiguous paths exist. A by-product of this is information on the range of complexity of the underlying gene families present. As a demonstration of CStones ability to assemble high-quality contigs, and to label them in this manner, both simulated and real data were used. For simulated data, ten million read pairs were generated from cDNA libraries representing four species, Drosophila melanogaster, Panthera pardus, Rattus norvegicus and Serinus canaria. These were assembled using CStone, Trinity and rnaSPAdes; the latter two being high-quality, well established, de novo assembers. For real data, two RNA-Seq datasets, each consisting of ≈30 million read pairs, representing two adult D. melanogaster whole-body samples were used. The contigs that CStone produced were comparable in quality to those of Trinity and rnaSPAdes in terms of length, sequence identity of aligned regions and the range of cDNA transcripts represented, whilst providing additional information on chimerism. Here we describe the details of CStones assembly and classification process, and propose that similar classification systems can be incorporated into other de novo assembly tools. Within a related side study, we explore the effects that chimera’s within reference sets have on the identification of differentially expression genes. CStone is available at: https://sourceforge.net/projects/cstone/.

Conference(s)
A poster that was presented at ISMB and at GenomePT is available here.

Getting Started
The [Quick Start] explains how to download and run the software as well as obtain test data and source code.

Funding
This work was funded by National Funds through Portuguese Foundation for Science and Technology (FCT - Fundação para a Ciência e a Tecnologia) and FEDER through the Operational Programme for Competitiveness Factors (COMPETE) under the references POCI-01-0145-FEDER-029115 and PTDC/BIA-EVL/29115/2017.

General detail on this project are available here.

Related Software

1. CStone < (current location)
2. CSReadGen
3. CView
4. ChimSim
5. TVScript

**| linkedIn | web | orcid | **
| linheiro . web . orcid |---| archer . web . orcid |

Licence and Disclaimer

This software is free and open-source software released under the GNU General Public License (GPL).

The software is provided "as is" and without warranty. It may contain errors or produce incorrect results. Users are responsible for evaluating the software and independently verifying any results before relying upon them, particularly for scientific, medical, or other consequential purposes.

To the extent permitted by applicable law, the author accepts no liability for any loss, damage, or other consequence arising from the use of this software.

Java Runtime

The software is intended to run on OpenJDK or another freely available Java Runtime Environment (JRE) or Java Development Kit (JDK) providing the required Java functionality. Compatibility may vary between Java versions and implementations. Third-party libraries or data included with or used by the software may be subject to their own licences and conditions.