best programs for alignment of large whole genomes?

Question

[vulpecula]

Hi everyone,

I have a near-chromosome level assembly of a mammal genome that I would like to attempt to align/assign the scaffolds to the most closely related and assembled domestic species and possibly compare it with other closely related species. I have previously used Satsuma to create synteny plots (visualized with circos), but with much smaller genomes (and its been awhile!). Does anyone have any suggestions for a good protocol/program/approach on this?

Thanks!

[h.mon]

LAST also can be used to align mammalian-sized genomes. However, unless the genomes you want to align are close, for synteny it is probably better to quickly predict genes and align the genes from one species to the genome of the other, then infer synteny from the gene order.

[WouterDeCoster]

Mummer or minimap2 can do that.

[Joe]

If you just want to view synteny, sibelia is a neat little tool too.

[Sej Modha]

I had used Synima recently for syntenic comparison of multiple Plasmodium genomes and thought that it produced nice figures too.

[vulpecula]

Hi all, I just wanted to follow up in case anyone else runs into this problem. I used LASTZ for this and ran the scaffolds in parallel. But, it worked very well. Thank you for your suggestions!