Hi all,
After a metagenome 16S microbiome project, we have been interested to whole sequence a bacteria genome of our interest in 3 different subjects.
Now I have 3 whole genomes of the same bacteria (belong to 3 different subjects) and I would like to compare those with the public annoted genome of the same bacteria. The sequences have been obtained on a 454 run. What tool do you suggest to use, what type of workflow?
On my experience, I would first try an assebly with gsAssembler and than a mapping with the gsMapper, but I don't know if it's the correct way and above all after that I don't know how to handle the large amount of data generated (for example I am interested in looking for changes in crucial genes that may cause a switch bethween a pathogen version of the bacteria).
I hope you have any idea on how proceed. Any input it's higly appreciated.
Thanks in advance,
Giorgio
After a metagenome 16S microbiome project, we have been interested to whole sequence a bacteria genome of our interest in 3 different subjects.
Now I have 3 whole genomes of the same bacteria (belong to 3 different subjects) and I would like to compare those with the public annoted genome of the same bacteria. The sequences have been obtained on a 454 run. What tool do you suggest to use, what type of workflow?
On my experience, I would first try an assebly with gsAssembler and than a mapping with the gsMapper, but I don't know if it's the correct way and above all after that I don't know how to handle the large amount of data generated (for example I am interested in looking for changes in crucial genes that may cause a switch bethween a pathogen version of the bacteria).
I hope you have any idea on how proceed. Any input it's higly appreciated.
Thanks in advance,
Giorgio
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