open source s/w to asssemble de novo assembly generated contigs using reference genom

[ajagannath.patro]

Is there any open source assembly softwares that takes in de novo assembly generated contigs and reference genome to produce bigger contigs( reference guided de novo assembly)?

Long question:

I have done de novo assembly of a chicken line using velvet(n50=35243, contigs=217304). I want to do some analysis on retroviral elements so I am using ltr_harvest for it. As these are repeat elements the length parameters are generally high but due to this many short contigs are filtered out and tend to loose a lot of information. So i am planning to use the contigs and reference genome to create bigger contigs. I have found one tool on it called alignGraph and I am testing it. Is there any open source assembly softwares that takes in de novo assembly generated contigs and reference genome to produce bigger contigs?

Thanks.

[cs]

try MIRA - http://mira-assembler.sourceforge.ne...ideToMIRA.html

[dutilh]

Yes, scaffold builder does exactly that: http://sourceforge.net/projects/scaffold-b/
it also has a web version, see http://edwards.sdsu.edu/scaffold_builder
See http://www.scfbm.org/content/8/1/23/abstract for the citation.

[ajagannath.patro]

thanks @cs and @dulith for the reply. I will try them out. Scaffold builder may be the answer

[EricSchon]

What was your experience with these tools (AlignGraph, mira, scaffold builder)? Which one did you end up using? I am similarly hoping to improve my denovo assembly, using a close reference genome