2 strains.De novo or resequencing?

[chariko]

Hello,

I am interested in sequencing 2 related strains of a Gram Negative bacteria, one sensible and the other resistant to multiple antibiotics in order to detect the mechanisms of resistance. I am not sure about the best method to apply:

1) Sequence de novo the sensible one and resequence the resistant one using the sensible as reference.
2) Sequence both strains de novo and afterwards compare them.

I think if I choose the first option I just be able to detect mutations or deletions but I won´t be able to detect new insertions in my resistant genome as well as they won´t align with my sensible reference strain. This option will be cheaper.

If I choose the second option I will be able to detect everything but it will be more expensive.

Which option would you recommend? Any other suggestions will be appreciated.

[westerman]

Both. The actual costs of sequencing will be small -- bacterial genome runs are easily less than $1000 these days. Once you have both sequenced then you can computationally do de-novo on both as well as use one as a reference and map the other and vice-versa. I suspect that the computer cost of doing this will be small.

I am all for saving money but if you are considering such small costs as bacterial sequencing as a barrier to your research then you really need to rethink what you trying to accomplish.