transXpress

transXpress performs de novo transcriptome assembly and annotation to process RNA-seq data from non-model organisms and support discovery of novel genes and proteins.

Key Features:

• Support for Multiple Assembly Programs: Compatible with Trinity and rnaSPAdes for de novo transcriptome assembly.
• Parallel Execution on Heterogeneous Clusters: Supports parallel execution across heterogeneous cluster computing environments for scalable processing.
• Automated Best-Practice RNA-seq Processing: Automates best-practice RNA-seq processing steps within the workflow.
• Standardized Output Formats: Produces standardized output files to enhance interoperability with downstream tools.

Scientific Applications:

• De novo transcriptome assembly and annotation: Enables assembly and annotation when reference genomes are absent for non-model organisms.
• Novel gene and protein discovery: Aids identification of novel genes and proteins from assembled transcriptomes.
• Downstream mining and characterization: Generates standardized outputs compatible with tools such as SequenceServer for mining and characterization of genetic elements.

Methodology:

Implemented as a Snakemake workflow that integrates RNA-seq data processing steps into a unified, reproducible, and modular pipeline producing standardized output formats.