Whole genome sequencing

[navik]

Hello All,

I have genome sequence from two inbred/varieties and reference genome is assembled and available. Wondering, what can I do with this sequence data to get useful information that aids plant breeding? Please reply if you have any thoughts.

Thanks,
Navik

[fjrossello]

Hi Navik,

Perform a QA/QC of your raw reads first. Then, If a reference genome is available, I would align your raw sequences first using a read aligner such as bwa or bowtie. Bear in mind that you will need to index your genome first.
You could later look for SNPs, compare differences between varieties, etc.
By the way, What sequencing platform have you used?

If you could give me more information I may be able to give you more accurate advise.

Cheers,

Fernando