Inquiry about Integrating Minigraph-cactus into the Pipeline for Enhanced SV Analysis

[porkfan]

Dear Guillaume Bourque's group,

Firstly, I would like to express my sincere gratitude for your remarkable software. It is indeed a significant contribution to the field. I've been using your pipeline for SV (Structural Variant) analysis, but I've encountered some intriguing differences in the results when comparing two methods.

I have been generating pan-genome SVs using Minigraph-cactus and also calling SVs based on your pipeline that utilizes svim for comparison against a reference genome. In my tests, I've observed that the alignment results from Minigraph-cactus seem to be more reliable.

Given these observations, I am curious about the possibility of integrating the Minigraph-cactus process into your pipeline. Specifically, I am interested in using the SVs generated by Minigraph-cactus and then applying your TE (Transposable Element) identification process for further analysis and genotyping.

I believe that the incorporation of Minigraph-cactus into your pipeline could enhance the accuracy and efficacy of SV analysis. Could you please let me know if such integration is feasible in your future development plans?

Your guidance and insights on this matter would be greatly appreciated.

Thank you for your time and consideration.

Best regards, Yfchen