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Old 01-11-2015, 09:50 PM   #1
ajagannath.patro
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Default open source s/w to asssemble de novo assembly generated contigs using reference genom

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.
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Old 01-12-2015, 01:25 AM   #2
cs
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try MIRA - http://mira-assembler.sourceforge.ne...ideToMIRA.html
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Old 01-12-2015, 08:03 AM   #3
dutilh
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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.
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Old 01-12-2015, 08:25 PM   #4
ajagannath.patro
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thanks @cs and @dulith for the reply. I will try them out. Scaffold builder may be the answer
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Old 04-29-2015, 04:16 AM   #5
EricSchon
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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
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