[HTML][HTML] Tools for building de novo transcriptome assembly

M Geniza, P Jaiswal - Current Plant Biology, 2017 - Elsevier
The availability of RNA-Seq method allows researchers to capture the spatial or temporal
profile of transcriptomes from various types of biological samples. The transcriptome data …

Trans2express – de novo transcriptome assembly pipeline optimized for gene expression analysis

AM Kasianova, AA Penin, MI Schelkunov, AS Kasianov… - Plant Methods, 2024 - Springer
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 …

The 'TranSeq'3′‐end sequencing method for high‐throughput transcriptomics and gene space refinement in plant genomes

O Tzfadia, S Bocobza, J Defoort… - The Plant …, 2018 - Wiley Online Library
High‐throughput RNA sequencing has proven invaluable not only to explore gene
expression but also for both gene prediction and genome annotation. However, RNA …

RNA-seq assembly–are we there yet?

S Schliesky, U Gowik, APM Weber… - Frontiers in plant …, 2012 - frontiersin.org
Transcriptomic sequence resources represent invaluable assets for research, in particular
for non-model species without a sequenced genome. To date, the Next Generation …

RNA-Seq for transcriptome analysis in non-model plants

R Garg, M Jain - Legume Genomics: Methods and Protocols, 2013 - Springer
Sequencing of mRNA using next-generation sequencing (NGS) technologies (RNA-seq)
has the potential to reveal unprecedented complexity of the transcriptomes. The …

[PDF][PDF] Plant transcriptome assembly: review and benchmarking

S Behera, A Voshall - Bioinformatics, 2022 - par.nsf.gov
Transcriptome assembly using next-generation sequencing data is an important step in a
wide range of biological studies at the molecular level. The quality of computationally …

Analysis of RNA-Seq data using TopHat and Cufflinks

S Ghosh, CKK Chan - Plant Bioinformatics: Methods and Protocols, 2016 - Springer
The recent advances in high throughput RNA sequencing (RNA-Seq) have generated huge
amounts of data in a very short span of time for a single sample. These data have required …

Bioinformatics challenges in de novo transcriptome assembly using short read sequences in the absence of a reference genome sequence

E Góngora-Castillo, CR Buell - Natural product reports, 2013 - pubs.rsc.org
Plant natural product research can be facilitated through genome and transcriptome
sequencing approaches that generate informative sequence and expression datasets that …

A pipeline for non-model organisms for de novo transcriptome assembly, annotation, and gene ontology analysis using open tools: case study with scots pine

GT Duarte, PY Volkova, SA Geras'kin - Bio-protocol, 2021 - bio-protocol.org
RNA sequencing (RNA-seq) has opened up the possibility of studying virtually any organism
at the whole transcriptome level. Nevertheless, the absence of a sequenced and accurately …

Designing a transcriptome next‐generation sequencing project for a nonmodel plant species1

SR Strickler, A Bombarely… - American journal of …, 2012 - Wiley Online Library
The application of next‐generation sequencing (NGS) to transcriptomics, commonly called
RNA‐seq, allows the nearly complete characterization of transcriptomic events occurring in …