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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)?

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.

assembly alignment sequencing
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updated by tuan.vietnguyen90 • tuan.vietnguyen90 • written by ajagannath.patro • ajagannath.patro

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

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written by st.ph.n st.ph.n

1 answer

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

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updated by Ram Ram • written by tuan.vietnguyen90 • tuan.vietnguyen90

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

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written by st.ph.n st.ph.n

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