Combining two different assemblies

yekwah · 07-14-2013, 06:23 PM

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 · 07-27-2013, 06:12 AM

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

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07-14-2013, 06:23 PM	#1
yekwah Junior Member Location: Melbourne, Victoria Join Date: Apr 2013 Posts: 6	Combining two different assemblies 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?

07-27-2013, 06:12 AM	#2
boetsie Senior Member Location: NL, Leiden Join Date: Feb 2010 Posts: 245	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