given the importance of transcriptome analysis in various biological studies and considering thevast amount of whole transcriptome sequencing data, it seems necessary to develop analgorithm to assemble transcriptome data. in this study we propose an algorithm fortranscriptome assembly in the absence of a reference genome. first, the contiguous sequencesare generated using de bruijn graph with d...

Given the importance of transcriptome analysis in various biological studies and considering thevast amount of whole transcriptome sequencing data, it seems necessary to develop analgorithm to assemble transcriptome data. In this study we propose an algorithm fortranscriptome assembly in the absence of a reference genome. First, the contiguous sequencesare generated using de Bruijn graph with d...

transition from vegetative to reproductive growth is an important stage in plant’s life. flowering pathways including photoperiod, vernalization, gibberellins, and autonomous pathway are regulated by different genes. identification of flowering genes is essential for the development of bolting-resistant sugar beet cultivars. in this study, a set of 118 arabidopsis thaliana genes involved in flo...

The transcriptome of triangle sail mussel Hyriopsis cumingii (Lea) using Illumina paired-end sequencing technology was conducted and analyzed. Equal quantities of total RNA isolated from six tissues, including gonads, hepatopancreas, foot, mantel, gills and adductor muscles, were pooled to construct a cDNA library. A total of 58.09 million clean reads with 98.48 % Q20 bases were generated. Clus...

A recommendation of: Ramon E Rivera-Vicens, Catalina Garcia-Escudero, Nicola Conci, Michael Eitel, Gert Wörheide TransPi - a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly https://doi.org/10.1101/2021.02.18.431773

Advent of Next Generation Sequencing has led to possibilities of de novo transcriptome assembly of organisms without availability of complete genome sequence. Among various sequencing platforms available, Illumina is the most widely used platform based on data quality, quantity and cost. Various de novo transcriptome assemblers are also available today for construction of de novo transcriptome....

Background. The emergence of next-generation sequencing platform gives rise to a new generation of assembly algorithms. Compared with the Sanger sequencing data, the next-generation sequence data present shorter reads, higher coverage depth, and different error profiles. These features bring new challenging issues for de novo transcriptome assembly. Methodology. To explore the influence of thes...

De novo assembled transcriptomes, in combination with RNA-Seq, are powerful tools to explore gene sequence and expression level in organisms without reference genomes. Investigators must first choose which high throughput sequencing platforms will provide data most suitable for their experimental goals. In this study, we explore the utility of 454 and Illumina sequences for de novo transcriptom...