Possible introduction of bias from reference from genome

[jeff-godwin]

Hi Alonge,

Thanks for this wonderful tool. We used ragtag correction for scaffolding our draft genome (plant) with a published genome of the same species, albeit from a different population. We got some very useful information and a slightly improved genome. During the publication process, one of the reviewers has commented on the draft genome becoming biased towards the reference genome as a result of this scaffolding process and mentioned how all downstream annotation will be affected as a result of this.

Our position is that ragtag merely re-orients the assembly sequences and the "uniqueness" (unique sequences) of the draft genome is still retained post the scaffolding. We are also planning to validating the results using optical mapping. We would be interested to know your thoughts on this. Is this a genuine caveat of reference based scaffolding?

Many thanks, Jeff