Combining two different assemblies

[yekwah]

Just wondering if anyone knows of any programs which can combine two different assemblies?

I've got paired end Illuminia data that I've assembled using Velvet and SPAdes. Once I fiddled with some of the SPAdes kmer settings I managed to get mostly better assemblies than I had with Velvet. However, SPAdes isn't consistently better - what I'd really like to do is combine the Velvet and SPAdes assemblies. I've found a few programs that will extract a non redundant set of contigs from two assemblies, but what I'd really rather have is a program which will do things like realise that a contig from Velvet and one from SPAdes overlap significantly and so merge the two together into one larger contig.

Any ideas?

[boetsie]

There is an old thread for merging assemblies, have a look at it here;

http://seqanswers.com/forums/showthread.php?t=10834&

I think the tool Zorro would be the best bet. I did not use it myself however.

Boetsie