CStone: A de novo assembler that identifies non-chimeric contig sequences based on underlying graph structure.

Conference Details: 

ISMB/ECCB, 25th - 30th July 2021, Virtual (url)

AND

GenomePT, 7th July, Virtual (url)

The poster is based on a paper titled "CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure" that is available here.

Presented by John Archer.

Poster Abstract:

Artificially generated chimeric sequences can closely resemble underlying expressed trans- cripts, but patterns such as those seen between co-evolving sites or re-mapped read counts become obscured. With the exponential growth of sequence information stored over the last decade the quantification of chimeras has become essential, especially when assembling read data. We have created a lenient de Bruijn based de novo assembler, CStone, that annotates each contig produced with one of three 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 demonstration of CStones ability to assemb- le high quality contigs, and to label them in this manner, RNA-Seq data was simulated from cDNA libraries representing ten different species and assembled using three different assem- blers: CStone, Trinity [1] and rnaSPAdes [2], On comparison back to the original cDNA libraries the contigs that CStone generates are comparable in quality to those of Trinity and rnaSpades, while providing additional information on chimerism. The CStone project is available at: ht- tps://sourceforge.net/projects/cstone/.

Related software to this project are:
1. CStone <
2. CSReadGen
3. CView
4. ChimSim
5. TVScript

A related poster discussing the effects of chimerism is available here.

General details of the project are available here.