Trans2express - de novo transcriptome assembly pipeline optimized for gene expression analysis.

ABSTRACT:

Background

As genomes of many eukaryotic species, especially plants, are large and complex, their de novo sequencing and assembly is still a difficult task despite progress in sequencing technologies. An alternative to genome assembly is the assembly of transcriptome, the set of RNA products of the expressed genes. While a bunch of de novo transcriptome assemblers exists, the challenges of transcriptomes (the existence of isoforms, the uneven expression levels across genes) complicates the generation of high-quality assemblies suitable for downstream analyses.

Results

We developed Trans2express - a web-based tool and a pipeline of de novo hybrid transcriptome assembly and postprocessing based on rnaSPAdes with a set of subsequent filtrations. The pipeline was tested on Arabi

SUBMITTER: Kasianova AM 

PROVIDER: S-EPMC11330051 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature