Question about assembly of repeat/non-coding regions in SPAdes

[microbpro-cat]

Hi, thank you for developing SPAdes.
I have a question about how your assembler handles repeat regions and non-coding regions, especially in mitochondrial genome assembly.

What is the main principle or algorithm for assembling repeat (or long non-coding) regions in SPAdes?

Are there specific heuristics, parameters, or steps used for resolving such regions?

Are there any known limitations or potential pitfalls when assembling repeat/non-coding regions with your tool?

If there is any official documentation or publication describing this, I would really appreciate a reference.

Thank you!

[asl]

Hello

Please refer to the following articles on repeat resolution:

• https://pmc.ncbi.nlm.nih.gov/articles/PMC4058921/
• https://academic.oup.com/bioinformatics/article/31/20/3262/195494