Hello everyone,
Here's the context: We have three plant species, namely species A, species B, and species C. Our goal is to identify the ancestral species that contributed to the development of species C. Our initial hypothesis suggests that species A and species B could be the contributors. To investigate this, we plan to conduct an identity-by-descent (IBD) analysis.
We have the following data available for the analysis:
- Complete genome assemblies for the three species, A, B, and C (unphased assembly).
In my research, I came across two tools, HapFabia (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905877/) and iLASH (https://www.nature.com/articles/s41467-021-22910-w), that might be helpful for this analysis. However, as a novice in this field, I find it challenging to understand how to perform these analyses effectively. Therefore, I'm seeking assistance from the experts in the community to gain a clearer understanding.
An explanation of the IBD analysis process, tailored to beginners, would be greatly appreciated.
Considering the analysis I wish to perform and the available data, I have several questions:
- What are the detailed steps to execute the IBD analysis using either HapFabia or iLASH?
- Do I need any additional data to conduct this analysis successfully?
- How do I prepare the input data for HapFabia or iLASH?
- Are there any other specific considerations or best practices I should be aware of?
I sincerely appreciate any help, advice, or guidance you can provide. Thank you in advance for your valuable support!
Best regards,
Alexis
