Go Back   SEQanswers > Applications Forums > De novo discovery

Similar Threads
Thread Thread Starter Forum Replies Last Post
Combining FPKM values for a gene john_nl Bioinformatics 5 02-16-2012 12:28 AM
Combining multiple Trinity assemblies? yeaman Bioinformatics 2 12-08-2011 05:30 PM
Comparing and combining vcf files gavin.oliver Bioinformatics 3 11-30-2011 03:16 AM
Combining *.gtf files? jhb1980 Bioinformatics 2 11-01-2011 01:43 AM
Combining data from 2 lines suludana Illumina/Solexa 1 01-09-2009 09:37 AM

Thread Tools
Old 07-14-2013, 06:23 PM   #1
Junior Member
Location: Melbourne, Victoria

Join Date: Apr 2013
Posts: 6
Default 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?
yekwah is offline   Reply With Quote
Old 07-27-2013, 06:12 AM   #2
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;

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

boetsie is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 11:59 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2015, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO