Generating Reference Sequence For Genome Wide Variation Study

Question

[ruru]

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,

Answer 1

[Istvan Albert]

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.