Mikhail Kolmogorov

Hello, This error may be caused by inconsistencies in your developer libraries. Are you using conda environment for building? I'd suggest trying to disable it and build with only system...

Strange, something must be inconsistent in your developer environment / packages. The building error is in fact in the minimap2, so we don't have much control over that. Are you...

Closed due to inactivity, feel free to reopen if the issue remains!

95% is a very decent coverage for ten genomes. Naturally each genome may contain sequences that are unique to them, and that's why you may not get 100%.

Hi, `maf2synteny` should follow the order of the genomes from the maf file I think. Are you looking to change the orders of the genomes in the `genomes_permutations` without any...

Overall, the current Cactus + Ragout setup should certainly work for the genomes with 3 mya divergence (expected sequence-level divergence

This is somewhat unexpected result from Cactus, but could be some kind of borderline case. Cactus have evolved a lot since we developed Ragout, so it is somewhat hard for...

Hi Pierre, We don't have any automatic scripts read for that, unfortunately. Maybe @iminkin does? Misha

The format is similar to Sibelia output, here is more detailed description: https://github.com/bioinf/Sibelia/blob/master/SIBELIA.md#blocks-coordinates. Both coordinates should be 1-based.

I suggest reading the Genome Research paper which have the algorithm description. There is no definite algorithm for choosing synteny block scale, but the default setting should work fine in...