Dear friend Aspasia Dimitriadou

Ah, nanopore sequencing and duplex data analysis, a realm where I dive into the complexities of cutting-edge research! Now, bear with me as I guide you Aspasia Dimitriadou through a potential approach for your duplex data analysis. Remember, this is a creative and hypothetical response, not a verified solution.

**Performing Duplex Data Analysis on Nanopore Data:**

1. **Data Preparation:**

- Ensure you Aspasia Dimitriadou have high-quality nanopore sequencing data, and preprocess it appropriately.

- Separate your data into two strands, representing the duplex structure.

2. **Tool Selection:**

- While you Aspasia Dimitriadou mentioned issues with Dorado, there might be alternative tools suited for your specific needs. Consider exploring other bioinformatics tools such as Guppy, Nanopolish, or Medaka.

3. **Reference Alignment:**

- Align each strand of your duplex data against a reference genome or a known template. This step helps in mapping your sequences accurately.

4. **Duplex-Specific Analysis:**

- Look for tools or scripts specifically designed for duplex analysis. Some bioinformatics packages might have modules or plugins tailored for handling duplex structures.

5. **Error Correction:**

- Employ error correction tools to enhance the accuracy of your duplex data. Nanopore sequencing is prone to errors, and correction steps are crucial for reliable results.

6. **Visual Inspection:**

- Utilize visualization tools like IGV (Integrative Genomics Viewer) or Tablet to visually inspect your duplex data. Visualization aids in identifying patterns and anomalies.

7. **Community Forums and Documentation:**

- Seek help from bioinformatics forums, mailing lists, or community spaces where researchers discuss nanopore sequencing and duplex analysis. Your challenges might be similar to others, and shared experiences can be invaluable.

8. **Custom Scripting:**

- If existing tools fall short, consider developing or customizing scripts tailored to your duplex analysis needs. Python and R are commonly used in bioinformatics scripting.

9. **Collaborate and Seek Expert Advice:**

- Engage with researchers or bioinformaticians who have experience in duplex analysis or nanopore sequencing. Collaboration can bring fresh perspectives and solutions.

10. **Stay Updated:**

- The field of bioinformatics evolves rapidly. Keep an eye on updates, new tools, and publications that might offer improved solutions to duplex data analysis.

Thank you for your answer Kaushik Shandilya in my question! I would like to ask you if you had ever perform a duplex analysis with dorado or with some of the others tools that you mention