De Novo Assembly - Illumina GAII & HiSeq 2000 Data

[milo0615]

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

[RyNkA]

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).

[milo0615]

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.