HPC-T-Assembly

HPC-T-Assembly performs de novo transcriptome assembly from RNA-seq data on high-performance computing (HPC) infrastructures for large multi-species datasets of non-model organisms.

Key Features:

• Multi-species configuration: Supports analysis configuration for simultaneous assemblies of RNA-seq data from several species.
• Automated parallel computing generation: Automatically generates parallel computing software for assembly once configuration data is provided.
• Assembly quality control: Includes post-processing steps for assessing assembly quality as part of intermediate and final outputs.
• ORF prediction: Performs open reading frame prediction as an additional post-processing step.
• Transcript count matrix construction: Generates transcript count matrices as part of the pipeline outputs.
• HPC deployment: Generates software that can be launched on a supercomputer with a simple command line to significantly reduce computational load and execution times.

Scientific Applications:

• Non-model organism transcriptomics: Enables de novo transcriptome assembly for organisms lacking well-annotated reference genomes as an alternative cost-effective protocol for differentially expressed genes (DEGs) analysis.
• Large-scale transcriptomic projects: Supports large-scale transcriptomic analysis projects through reduced computational load and execution times on HPC infrastructures.
• Meta-transcriptomics: Enables meta-transcriptomics analysis projects through parallel pipeline execution on HPC infrastructures.

Methodology:

The pipeline automatically generates parallel computing software for de novo transcriptome assembly after user configuration, with post-processing steps including assembly quality control, ORF prediction, and transcript count matrix construction.