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Old 05-02-2014, 03:57 PM   #1
milo0615
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Location: Walnut, California

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Default De Novo Assembly - Illumina GAII & HiSeq 2000 Data

Hello,

I have successfully assembled Illumina GA II and Illumina HiSeq 2000 data using ABySS for various K-mers. However, I would like to know if there is a way to combine both Illumina GAII & Illumina HiSeq data and re-assemble it. Should I combine the Illumina data or their respective Kmer? Can ABySS re-assemble an already assembled data? I would really appreciate your help.


Thank you,

-Milo
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Old 05-04-2014, 06:05 PM   #2
RyNkA
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Quote:
Originally Posted by milo0615 View Post
Hello,

I have successfully assembled Illumina GA II and Illumina HiSeq 2000 data using ABySS for various K-mers. However, I would like to know if there is a way to combine both Illumina GAII & Illumina HiSeq data and re-assemble it. Should I combine the Illumina data or their respective Kmer? Can ABySS re-assemble an already assembled data? I would really appreciate your help.


Thank you,

-Milo
It is possible to combine 2 different dataset and do an assembly.

However, don't re-assemble an already assembled data, that will mess up the data a lot. So in this sense, your choice can be combine the illumina raw data, do QC, and try the assembly again . For post-assembly process, in my opinion it might be okay to do a clustering by cdhit or tgicl (not really popular).
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Old 05-09-2014, 04:02 PM   #3
milo0615
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Originally Posted by RyNkA View Post
It is possible to combine 2 different dataset and do an assembly.

However, don't re-assemble an already assembled data, that will mess up the data a lot. So in this sense, your choice can be combine the illumina raw data, do QC, and try the assembly again . For post-assembly process, in my opinion it might be okay to do a clustering by cdhit or tgicl (not really popular).
Hi RyNkA,

I am going to use ABySS to do a paired-end assembly of the multiple libraries. Thank you for your reply.
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