Enhancement Request: Handling Telomeric Segments During 3D-DNA Correction and Potential Strategies to Prevent Trimming

[Hanjiangna]

Dear 3D-DNA developers,

I have noticed that during the correction phase of the 3D-DNA pipeline, certain telomeric segments of contigs are sometimes trimmed. This appears to occur due to the inherent challenges associated with the highly repetitive nature of telomeric sequences and the complexity of assembling these regions accurately. It is also possible that incomplete coverage or ambiguous alignments in the sequencing data contribute to these regions being considered less reliable and consequently removed.

Could you kindly elaborate on the underlying reasons for this trimming behavior within the 3D-DNA correction algorithm?

Moreover, I'm curious to know if there are specific parameters or strategies currently available within the tool that can be optimized to improve the handling of telomeric regions during assembly. Are there recommended adjustments to prevent unnecessary loss of telomeric sequence information?

Looking forward, do you have plans to enhance the capability of 3D-DNA in dealing with telomeric assemblies in upcoming versions? It would be beneficial for the community to have improved support for accurate telomere reconstruction to ensure more complete and faithful representation of genomic sequences.

Thank you for your attention and looking forward to your response.

Best regards
han jiangna