TransRef enables accurate transcriptome assembly by redefining accurate neo-splicing graphs

Abstract

RNA-seq technology is widely employed in various research areas related to transcriptome analyses, and the identification of all the expressed transcripts from short sequencing reads presents a considerable computational challenge. In this study, we introduce TransRef, a new computational algorithm for accurate transcriptome assembly by redefining a novel graph model, the neo-splicing graph, and then iteratively applying a constrained dynamic programming to reconstruct all the expressed transcripts for each graph. When TransRef is utilized to analyze both real and simulated datasets, its performance is notably better than those of several state-of-the-art assemblers, including StringTie2, Cufflinks and Scallop. In particular, the performance of TransRef is notably strong in identifying novel transcripts and transcripts with low-expression levels, while the other assemblers are less effective.

Tiglon enables accurate transcriptome assembly via integrating mappings of different aligners

“…Moreover, each labeled paired path corresponds to a segment of an expressed transcript and should be covered by at least one predicted transcript. To achieve this goal, we strategically use the label information and the reliable labeled paired paths in the labeled splice graph and employ a new labeled-based dynamic programming algorithm that is similar to our previous study ( Yu et al., 2021 ) to generate the transcript-representing path cover over each labeled graph. In detail, we recover the expressed transcripts by the following steps.…”

QTL cluster analysis and marker development for kernel traits based on DArT markers in spring bread wheat (Triticum aestivum L.)

“…In our study, we found TaTKW-1A, which has two major candidate genes, TraesCS1A02G045300 and TraesCS1A02G058400, with grainrelated traits (Figure 7). We identified them in the transcriptome of wheat grain through the website https://www.ebi.ac.uk/gxa/home (Gillies et al, 2012;Li et al, 2013;Takafuji et al, 2021;Yu et al, 2021) (Figure S5). Results showed that both genes were expressed during grain development, although the expression profiles of these two genes clearly differ during grain development; both of them were expressed in the pericarp, endosperm, and seed coat (Li et al, 2013;Yu et al, 2021).…”

“…We identified them in the transcriptome of wheat grain through the website https://www.ebi.ac.uk/gxa/home (Gillies et al, 2012;Li et al, 2013;Takafuji et al, 2021;Yu et al, 2021) (Figure S5). Results showed that both genes were expressed during grain development, although the expression profiles of these two genes clearly differ during grain development; both of them were expressed in the pericarp, endosperm, and seed coat (Li et al, 2013;Yu et al, 2021). Specifically, TraesCS1A02G045300 is important because it was expressed consistently from anthesis to maturity (Pfeifer et al, 2014;Pearce et al, 2015;Yu et al, 2021).…”