CStone paper: Case study 1 - simulated data

Summary

cDNA libraries from fruit fly, leopard, rat and canary were downloaded from Ensembl [1]. For each ≈10 million read pairs, of length 200 nt, insert size 300 nt and containing no read error, were generated from transcripts that ranged in length from 300 to 5000 nt in a manner that reflects uniform coverage. Further details are described in our manuscript: "CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure" [2]. Use of such simulated data allows for the comparison of the assembled contigs to the sequences from which the reads were derived, while excluding the effects of unknown variation; including that of sequencing error and poor coverage. The CStone project page is located at: https://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 the identification of chimerism during assembly is available here and one discussing the effects of chimerism is available here.

General details of the project are available here.

References

1. Yates AD, Achuthan P, Akanni W, Allen J, Allen J, Alvarez-Jarreta J, et al. Ensembl 2020. Nucleic Acids Res. 2020;48: D682–D688. doi:10.1093/NAR/GKZ966

2. 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.