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  • 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!

  • #2
    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




    Let me know if that helps.

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