De-Novo Genome Assemblies Comparison

Question

[Coryza]

Hi,

I'm wondering if any of you have any good ideas to compare multiple genomes from different (plant) species on the same genus level assessing genome assembly quality. So far we've compared basic statistics (number of contigs, bases, N50 et cetera), and we have aligned a set of unigenes to see whether those can be found back and show concordance over the different assemblies.

Any of you have good ideas regarding comparison of genome assemblies qualities?

Thanks!

Answer 1

[Rayan Chikhi]

For a comprehensive set of metrics, take a look at these two previous threads:

How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)

Assessing The Quality Of De Novo Assembled Data

(Assemblathon 2 is a reference paper in the field)

Answer 2

[biogirl]

Have you tried QUAST?

It provides some great statistics on assemblies and funky plots too.

[Coryza]

Hi! Thanks for the input. QUAST was already indeed on my to-do list!

[Coryza]

Unfortunately QUAST did not help that much. It's basically in our case a visualization of N50 statistics and some other basic ones, which we had already computed ourselves.