Question: 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)?
2
gravatar for ajagannath.patro
4.9 years ago by
India
ajagannath.patro20 wrote:

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.

sequencing alignment assembly • 2.8k views
ADD COMMENTlink modified 4.9 years ago by tuan.vietnguyen900 • written 4.9 years ago by ajagannath.patro20

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

ADD REPLYlink written 4.9 years ago by st.ph.n2.5k
0
gravatar for tuan.vietnguyen90
4.9 years ago by
Australia
tuan.vietnguyen900 wrote:

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

ADD COMMENTlink modified 8 weeks ago by RamRS25k • written 4.9 years ago by tuan.vietnguyen900

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

ADD REPLYlink written 4.9 years ago by st.ph.n2.5k
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