Whole genome alignment graph building

Question

[samuel.a.odonnell]

Hi everyone

Just looking for suggestions on which is the best tool to try build a genome graph out of alignments from many de novo assemblies?

I have seen cactus used in the vg publication and see novograph as an alternative

Are there any others I am missing or specificities between cactus and novograph that I should be aware of?

Thank you

Samuel

[ac2278]

I'm also curious about what other whole genome aligners are out there and why the authors of the vg paper selected Cactus. Also, does anyone know why the authors of the vg paper used yeast as an example rather than human?

Answer 1

[glenn.hickey]

Another method in development is https://github.com/pangenome/pggb

We are also making some changes to cactus to make it easier and more practical to use for pangenomes (as opposed to interspecies alignments) -- look out for them in a release soon.