how to get the genome coverage of assembly result

[gridbird]

I want to get the genome coverage of assembly contigs.
This is a simulated dataset , so I have reference genome.
I got assembly contigs using Velvet, but I don't know how the contig is correct or wrong. If I using blast aligned the contigs to reference genomes, how do i decide the correct contig or wrong contig? if one contig part aligned to reference genome, how should I do?

thanks

[lcollado]

You can always aling your reads against your contigs and determine any inconsistencies. The group at the Broad Institute proposed in their ALLPATHS papers other ways to evaluate assemblies.

Leo

[Thorondor]

take a look at vmatch

http://www.vmatch.de/

[pari_89]

You can take a look at QUAST as well. It computes all the metrics.

http://sourceforge.net/projects/quast/

[AdrianP]

You want coverage for contigs? Use MIRA. It spits out a file called contig stats, where you got average coverage, max coverage, gc content and other info for every contig produced.