Abstract
RNA-seq data produced by next-generation sequencing technology is a useful tool for analyzing transcriptomes. However, existing de novo transcriptome assemblers do not fully utilize the properties of transcriptomes and may result in short contigs because of the splicing nature (shared exons) of the genes. We propose the T-IDBA algorithm to reconstruct expressed isoforms without reference genome. By using pair-end information to solve the problem of long repeats in different genes and branching in the same gene due to alternative splicing, the graph can be decomposed into small components, each corresponds to a gene. The most possible isoforms with sufficient support from the pair-end reads will be found heuristically. In practice, our de novo transcriptome assembler, T-IDBA, outperforms Abyss substantially in terms of sensitivity and precision for both simulated and real data. T-IDBA is available at http://www.cs.hku.hk/~alse/tidba/
This research is partly supported by RGC Grants.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Graveley, B.R.: Molecular biology: power sequencing. Nature 453, 1197–1198 (2008)
Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M., Snyder, M.: The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344–1349 (2008)
Trapnell, C., Pachter, L., Salzberg, S.L.: TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009)
Jiang, H., Wong, W.H.: Statistical inferences for isoform expression in RNA-Seq. Bioinformatics 25, 1026–1032 (2009)
Birol, I., Jackman, S.D., Nielsen, C.B., Qian, J.Q., Varhol, R., Stazyk, G., Morin, R.D., Zhao, Y., Hirst, M., Schein, J.E., Horsman, D.E., Connors, J.M., Gascoyne, R.D., Marra, M.A., Jones, S.J.: De novo transcriptome assembly with ABySS. Bioinformatics 25, 2872–2877 (2009)
Jackson, B.G., Schnable, P.S., Aluru, S.: Parallel short sequence assembly of transcriptomes. BMC Bioinformatics 10 Suppl 1, S14 (2009)
Peng, Y., Leung, H.C.M., Yiu, S.M., Chin, F.Y.L.: IDBA- A Practical Iterative de Bruijn Graph De Novo Assembler. In: Berger, B. (ed.) RECOMB 2010. LNCS, vol. 6044, pp. 426–440. Springer, Heidelberg (2010)
Guttman, M., Garber, M., Levin, J.Z., Donaghey, J., Robinson, J., Adiconis, X., Fan, L., Koziol, M.J., Gnirke, A., Nusbaum, C., Rinn, J.L., Lander, E.S., Regev, A.: Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 28, 503–510 (2010)
Simpson, J.T., Wong, K., Jackman, S.D., Schein, J.E., Jones, S.J., Birol, I.: ABySS: a parallel assembler for short read sequence data. Genome Res. 19, 1117–1123 (2009)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Peng, Y., Leung, H.C.M., Yiu, S.M., Chin, F.Y.L. (2011). T-IDBA: A de novo Iterative de Bruijn Graph Assembler for Transcriptome. In: Bafna, V., Sahinalp, S.C. (eds) Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science(), vol 6577. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-20036-6_31
Download citation
DOI: https://doi.org/10.1007/978-3-642-20036-6_31
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-20035-9
Online ISBN: 978-3-642-20036-6
eBook Packages: Computer ScienceComputer Science (R0)