SSP: An interval integer linear programming for de novo transcriptome assembly and isoform discovery of RNA-seq reads

• Reconstruction of transcriptome sequence is a challenging task.
• A novel de novo method using interval integer linear programming is developed.
• The performance of method is almost similar or greater than the other de novo methods.
• This method estimates the expression level of reconstructed transcripts.
• Analysis suggests that the results are independent of the coverage of transcripts.

Recent advances in the sequencing technologies have provided a handful of RNA-seq datasets for transcriptome analysis. However, reconstruction of full-length isoforms and estimation of the expression level of transcripts with a low cost are challenging tasks. We propose a novel de novo method named SSP that incorporates interval integer linear programming to resolve alternatively spliced isoforms and reconstruct the whole transcriptome from short reads. Experimental results show that SSP is fast and precise in determining different alternatively spliced isoforms along with the estimation of reconstructed transcript abundances. The SSP software package is available at http://www.bioinf.cs.ipm.ir/software/ssp.