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.
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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