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Velvet will take long reads and short paired reads in the same assembly. It's described in the current manual pg. 8, "Adding long reads". -
Scaffolding problem
Hi,
I have these scaffolds with different sizes(1 to 200 kb) from a previous assembly.
Now there is some new data with 3 and 5kb insert paired end. I want to add these paired end reads onto the scaffolds.
I tried SOAP denovo, but it only takes paired end reads or single reads. Same thing goes for velvet and abyss.
The data is too big for CAP3.
What other programs are able to handle this kind of data?
Thanks
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