This repository provides workflows for bulk Oxford Nanopore Technologies (ONT) transcriptomics analysis, designed to streamline the entire process using fastq.gz files as input. The input data is processed through the following steps:
- Pychopper: For trimming and identifying full-length transcripts.
- Minimap2: For mapping reads to the reference genome.
- Bambu: To generate gene- or transcript-level count matrices.
The pipeline also includes downstream analyses, such as:
- Differential transcript usage (DTU) analysis
- Protein domain search
- Protein alignment
The workflows are structured using CGAT's Ruffus pipeline framework and are currently built within the TallyTrin environment. For detailed installation instructions, please refer to TallyTrin.
For the R packages used in the workflows, please visit their respective GitHub pages for installation and further details.
Please check the pipeline.yml file of each pipeline for information on software requirements and the genome references needed for data processing.