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.
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.
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