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john@wurbio 05-23-2011 01:15 AM

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!

seb567 05-31-2011 09:18 AM

Quote:

Originally Posted by john@wurbio (Post 42247)
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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