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)?

Question

[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.

[st.ph.n]

ABySS does report scaffolds for de novo genome assembly. I believe you can also do reference-guided.

Answer 1

[tuan.vietnguyen90]

If you still got the raw reads (i suppose you will anyway), why not try a genome guided de novo assembly using Trinity?

[st.ph.n]

Trinity is a de novo transcriptome assembler, for use with RNAseq data. @ajagannath.patro: Are you assembling a genome or transcriptome?