short-read sequence assemblies for variation detection

[C-YONG]

Hello Developers,

I've successfully built a pan-genome consisting of 7 fugu genomes using MC without any problems. Thank you for your kind descriptions on GitHub. Now, I'm planning to find more SVs by adding short-read sequence data.
Should I perform haplotype sampling or allele frequency filtering?
Should I just use CILP filtering?
Thank you for your support, and I look forward to hearing from you soon!

Best Regards

[glennhickey]

As shown here, haplotype sampling (--haplo) gives better performance than allele frequency filtering.

So my suggestion is to use the haplotype filtering, but since we only tested on human, I can't guarantee that it will outperform frequency filtering --filter 2 --giraffe on fugu.

[C-YONG]

Hello! Based on the content from the VG Giraffe best practices document :"With a small number of haplotypes (e.g. 10), the default graph is usually a good choice."
Does this mean we don’t need filtering（d2） or haplotype sampling?
I would like to understand whether such filtering or haplotype sampling is necessary for graphs constructed with a small number of genomes. For such simple graphs, is the default already sufficient?