[HTML][HTML] RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application
The study of RNA has been dramatically improved by the introduction of Next Generation
Sequencing platforms allowing massive and cheap sequencing of selected RNA fractions,
also providing information on strand orientation (RNA-Seq). The complexity of …
Sequencing platforms allowing massive and cheap sequencing of selected RNA fractions,
also providing information on strand orientation (RNA-Seq). The complexity of …
[HTML][HTML] TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation
Technical advances in Next Generation Sequencing (NGS) provide a means to acquire
deeper insights into cellular functions. The lack of standardized and automated
methodologies poses a challenge for the analysis and interpretation of RNA sequencing …
deeper insights into cellular functions. The lack of standardized and automated
methodologies poses a challenge for the analysis and interpretation of RNA sequencing …
TRUFA: A User-Friendly Web Server for de novo RNA-seq Analysis Using Cluster Computing
E Kornobis, L Cabellos, F Aguilar… - Evolutionary …, 2015 - journals.sagepub.com
Application of next-generation sequencing (NGS) methods for transcriptome analysis (RNA-
seq) has become increasingly accessible in recent years and are of great interest to many
biological disciplines including, eg, evolutionary biology, ecology, biomedicine, and …
seq) has become increasingly accessible in recent years and are of great interest to many
biological disciplines including, eg, evolutionary biology, ecology, biomedicine, and …
[HTML][HTML] Scalability and validation of big data bioinformatics software
This review examines two important aspects that are central to modern big data
bioinformatics analysis–software scalability and validity. We argue that not only are the
issues of scalability and validation common to all big data bioinformatics analyses, they can …
bioinformatics analysis–software scalability and validity. We argue that not only are the
issues of scalability and validation common to all big data bioinformatics analyses, they can …
RNA-seq analysis in forest tree species: bioinformatic problems and solutions
UL De Heredia, JL Vázquez-Poletti - Tree Genetics & Genomes, 2016 - Springer
Direct sequencing of RNA (RNA-seq) using next-generation sequencing platforms has
allowed a growing number of gene expression studies focused on forest trees in the last 5
years. Bioinformatic analyses derived from RNA-seq of forest trees are particularly …
allowed a growing number of gene expression studies focused on forest trees in the last 5
years. Bioinformatic analyses derived from RNA-seq of forest trees are particularly …
[HTML][HTML] Hermes: Seamless delivery of containerized bioinformatics workflows in hybrid cloud (HTC) environments
Hermes introduces a new “describe once, run anywhere” paradigm for the execution of
bioinformatics workflows in hybrid cloud environments. It combines the traditional features of
parallelization-enabled workflow management systems and of distributed computing …
bioinformatics workflows in hybrid cloud environments. It combines the traditional features of
parallelization-enabled workflow management systems and of distributed computing …
CAFU: a galaxy framework for exploring unmapped RNA-Seq data
A widely used approach in transcriptome analysis is the alignment of short reads to a
reference genome. However, owing to the deficiencies of specially designed analytical
systems, short reads unmapped to the genome sequence are usually ignored, resulting in …
reference genome. However, owing to the deficiencies of specially designed analytical
systems, short reads unmapped to the genome sequence are usually ignored, resulting in …
[HTML][HTML] Data-aware optimization of bioinformatics workflows in hybrid clouds
AM Kintsakis, FE Psomopoulos… - Journal of Big …, 2016 - journalofbigdata.springeropen.com
Life Sciences have been established and widely accepted as a foremost Big Data discipline;
as such they are a constant source of the most computationally challenging problems. In
order to provide efficient solutions, the community is turning towards scalable approaches …
as such they are a constant source of the most computationally challenging problems. In
order to provide efficient solutions, the community is turning towards scalable approaches …
MATHT: A web server for comprehensive transcriptome data analysis
W Song, H Liu, J Wang, Y Kong, X Yin… - Journal of theoretical …, 2018 - Elsevier
The current software/algorithms for high-throughput sequence data analysis are not user-
friendly. We developed MATHT, the Multifaceted Analysis Tool for Human Transcriptome,
which is a free web server available at www. biocloudservice. com, to provide more …
friendly. We developed MATHT, the Multifaceted Analysis Tool for Human Transcriptome,
which is a free web server available at www. biocloudservice. com, to provide more …
[PDF][PDF] Novel Methods for the Computational Analysis of RNA-Seq Data with Applications to Alternative Splicing
A Kahles - 2014 - d-nb.info
Understanding how genetic information is transformed into a diverse spectrum of complex
organisms is one of the longstanding questions of biology. Over the recent years,
advancements in sequencing technology have enabled the accurate measurement of the …
organisms is one of the longstanding questions of biology. Over the recent years,
advancements in sequencing technology have enabled the accurate measurement of the …