SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics
Similar Threads
Thread Thread Starter Forum Replies Last Post
Assisted de novo genome assembly? Create new consensus mapping reads to reference? zmartine Bioinformatics 8 02-10-2012 12:31 AM
Running assisted assemblies with runAssembly Broadie 454 Pyrosequencing 3 08-24-2011 12:31 AM
Bambus for scaffolding big genome?? shaohua.fan Bioinformatics 3 06-25-2011 08:41 AM
Assisted assembly of contigs into supercontigs/chromosomes lechu502 Genomic Resequencing 1 12-13-2010 04:56 AM
looking for reference assisted assembler recommendation sbberes Bioinformatics 0 10-14-2009 10:06 AM

Reply
 
Thread Tools
Old 08-10-2012, 01:16 PM   #1
sasignor
Member
 
Location: Davis, CA

Join Date: Sep 2009
Posts: 28
Default software for genome assisted scaffolding

Hello all,
I have genome assemblies for two closely related species, one of which is much more complete than the other (and which I did not assemble). I am trying to improve my assembly using the information from the other assembly, but can't seem to find any programs that do this. I assembled contigs using abyss, and then improved the assembly using SSPACE. There is still a lot of room for improvement with the information from the other assembly.

Recommendations?

Thanks!
sasignor is offline   Reply With Quote
Old 08-11-2012, 09:05 PM   #2
Torst
Senior Member
 
Location: The University of Melbourne, AUSTRALIA

Join Date: Apr 2008
Posts: 275
Default

Quote:
Originally Posted by sasignor View Post
I have genome assemblies for two closely related species, one of which is much more complete than the other (and which I did not assemble). I am trying to improve my assembly using the information from the other assembly
Have you tried using Mauve's "Contig Mover" to align/order/orient your "bad" draft contigs against your "good" draft contigs?

URL: http://asap.ahabs.wisc.edu/mauve-ali...t-genomes.html
Torst is offline   Reply With Quote
Old 08-13-2012, 11:08 AM   #3
sasignor
Member
 
Location: Davis, CA

Join Date: Sep 2009
Posts: 28
Default

I wasn't really looking for something that just reorders contigs, so much as uses an existing assembly to lower the threshold for joining contigs or to assist in the initial assembly.
sasignor is offline   Reply With Quote
Old 08-13-2012, 09:20 PM   #4
aaronrjex
Junior Member
 
Location: Australia

Join Date: Aug 2012
Posts: 7
Default

Columbus (which is an extension of Velvet: http://www.ebi.ac.uk/~zerbino/velvet/) seems to work quite well. Basically you align the reads from your query sequence to your reference sequence using a program like bwa, output a sam file and use this as the input for a Velvet assembly (the manual explains it all). I would suggest making sure your kmer_cov does not drop below 10 fold (Dan Zerbino does a much better job of explaining that one than I would be able to at http://www.ebi.ac.uk/~zerbino/velvet...th_choice.html).

Otherwise you could try the Sanger Institute's PAGIT pipeline (http://www.sanger.ac.uk/resources/software/pagit/), however that will probably only work if your reference assembly is of pretty high quality and you do not anticipate large rearrangements of the genome between the two sequences.

Hope that is of some use.
aaronrjex is offline   Reply With Quote
Old 08-14-2012, 04:08 PM   #5
sasignor
Member
 
Location: Davis, CA

Join Date: Sep 2009
Posts: 28
Default

Thanks!

My initial attempt used abyss to assemble the reads and SSPACE to improve the assembly. So far Columbus seems to be far, far worse than this which is odd. The input .sam file shows 93% of the reads being mapped to the reference but the output is much more fragmented than using abyss+SSPACE. It isn't a product of the reference as this is more complete. Perhaps I am not using the correct parameters.

./velveth my_dir 45 -reference genome.txt -shortPaired -sam sorted.sam

./velvetg my_dir -ins_length 350 -exp_cov auto -min_contig_lgth 300

PAGIT is still running, although it doesn't seem to do quite what I am looking for, but we'll see how it turns out.
sasignor is offline   Reply With Quote
Reply

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 03:48 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO