TRUFA Workflow
TRUFA
Overview
TRUFA stands for TRanscriptome User-Friendly Analysis, an informatics platform based on a web interface that generates the outputs commonly used in de novo RNA-seq analysis and comparative transcriptomics. TRUFA offer the next services, raw read cleaning executed, transcript assembly and annotation, and expression quantification. TRUFA is highly parallelized and benefits from the use of high performance computing resources. TRUFA gives the user an easy, fast and valid analysis on RNA-seq data.
Implementation
The platform is written using JavaScript, Python and Bash and it is currently installed in the ALTAMIRA supercomputer at the Instituto de Fisica de Cantabria(IFCA, Spain).The platform is highly parallelized both at the pipeline and program level, and can access up to 256 cores per execution instance for certain components of the pipeline.
Applications
TRUFA is designed to exclusively perform tasks related to de novo RNA-seq analysis, for this reason, the most important fields of application are evolutionary biology, ecology ,biomedicine and computational biology.
Conclusion
TRUFA provides a set of the most common tasks to perform a whole de novo RNA-seq analysis. It allows scientists which does not have bioinformatics skills or access to fast computing services. TRUFA works in an efficient, consistent and user-friendly manner, based on a pipeline approach. TRUFA integrates some widely used quality control programs in order to obtain optimization of the assembly process in the RNA-seq analysis.