Hai all,
My team have sequenced 3 genomes from similar crop but with different varieties. One of the variety is a parental lines. Would it be a good approach if I assemble the parental lines with scaffold from the draft genome? FYI, the draft genome is still not completed. My purpose of doing that is to use it as a reference sequences that will be aligned against 2 varieties. The objective of my study is to discover the SNP.
Thanks,
This is a difficult question to evaluate without the specifics. I would say that it all depends on the size and number of the contigs you have. If you are only interested in the SNPs putting all the effort into creating a parental line or scaffolding may not be necessary. You could just as well align against the contigs, then when you do find SNPs with sufficient evidence resolve them individually.
please add the above as a comment then delete it, right now you have added a new answer
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