This pipeline is designed to process Oxford Nanopore Technologies (ONT) sequencing reads and generate a summary report for selected samples. The report includes expected sequencing coverage and Bracken-based taxonomic analysis.
The pipeline requires the following inputs:
- A directory named pod5/ containing all .pod5 raw signal files.
- A sample sheet provided via the --file parameter. The sample sheet must list samples and their associated barcodes using a semicolon (;) as a separator. For example: 01;SAMPA 02;SAMPB The files .pod5 that are not associated to a barcode will be put in the directory excluded/
The pipeline supports optional DNA methylation analysis. The following models are available:
- 6mA
- 4mC
- 5mC
- 5mCG You can choose which methylation analysis to run. By default, this option is set to false.
The pipeline can optionally perform:
- Read alignment using the Dorado aligner
- Methylation extraction using Modkit pileup By default, this step is disabled (false).