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Old 05-23-2011, 01:15 AM   #1
john@wurbio
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Location: wageningen

Join Date: May 2011
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Default short read assembly

Hi all,

I have a rather unusual question for which I get conflicting answers up to know. Hope anyone can be of help.
We have made a RRLibrary of 100-200bp fragments for GA2 sequebcing. The forward run is 100bp and the reverse run -due to machine failure- only 45bp. How does this influence assembly compared to 100bp from both runs? Do we n
eed to adjust settings in a short read assembler?

Thanks!
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Old 05-31-2011, 09:18 AM   #2
seb567
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Location: Québec, Canada

Join Date: Jul 2008
Posts: 260
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Quote:
Originally Posted by john@wurbio View Post
Hi all,

I have a rather unusual question for which I get conflicting answers up to know. Hope anyone can be of help.
We have made a RRLibrary of 100-200bp fragments for GA2 sequebcing. The forward run is 100bp and the reverse run -due to machine failure- only 45bp. How does this influence assembly compared to 100bp from both runs? Do we n
eed to adjust settings in a short read assembler?

Thanks!
Hi !

I am the author of the Ray genome assembler.

With Ray, I can say that it does not matter.

To run Ray on your data:

mpirun -np 8 Ray -p forward.fastq reverse.fastq -o test-Ray-assembler


http://denovoassembler.sf.net

Let me know if that helps.
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