Hello,
I've been searching the forums for answers to this classic question, what is "best", de novo or mapping assembling.
Answers are somewhat vague as far as I could find (of course I might have missed good threads on the subject).
So I would like to ask it once more. Regarding bacterial genomes, 454 sequenced, plenty of references out there (known species). Our objective is to study a new pathotype, so we're looking for genes that might be novel and niche specific. In the end we have three pathogenic strains to compare to one non-pathogenic one, our negative control.
De novo? Mapping to ref. (and then de novo of unmapped reads, which are about 20%)?
Ideas? I'd appreciate a lot to hear from your experience.
Best,
SB
I've been searching the forums for answers to this classic question, what is "best", de novo or mapping assembling.
Answers are somewhat vague as far as I could find (of course I might have missed good threads on the subject).
So I would like to ask it once more. Regarding bacterial genomes, 454 sequenced, plenty of references out there (known species). Our objective is to study a new pathotype, so we're looking for genes that might be novel and niche specific. In the end we have three pathogenic strains to compare to one non-pathogenic one, our negative control.
De novo? Mapping to ref. (and then de novo of unmapped reads, which are about 20%)?
Ideas? I'd appreciate a lot to hear from your experience.
Best,
SB