Question: De-Novo Genome Assemblies Comparison
2
gravatar for Coryza
4.6 years ago by
Coryza380
Netherlands
Coryza380 wrote:

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!

assembly genome de-novo • 4.6k views
ADD COMMENTlink modified 4.6 years ago by biogirl160 • written 4.6 years ago by Coryza380
1
gravatar for Rayan Chikhi
4.6 years ago by
Rayan Chikhi1.4k
France, Lille, CNRS
Rayan Chikhi1.4k wrote:

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)

ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by Rayan Chikhi1.4k
0
gravatar for biogirl
4.6 years ago by
biogirl160
European Union
biogirl160 wrote:

Have you tried QUAST? (http://bioinf.spbau.ru/en/quast)

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

ADD COMMENTlink written 4.6 years ago by biogirl160

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

ADD REPLYlink written 4.6 years ago by Coryza380

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

ADD REPLYlink written 4.6 years ago by Coryza380
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