Hi,
I've got about 100 strains of E. Coli that should be sequenced and assembled. What is the best option for getting semi-complete genomes? My current thougts are to use >=100bp single read + 5kb mate pair.
As E. coli strains can differ quite a bit and we want to look at the differences between these strains both at genome (organizational) level and more local differences, I would guess that de novo assembly would be preferable if it can be done. Does anyone have experience with assembly of something like this? How is the quality of the genome compared to what you get with 454?
Cheers,
--
Einar Ryeng
I've got about 100 strains of E. Coli that should be sequenced and assembled. What is the best option for getting semi-complete genomes? My current thougts are to use >=100bp single read + 5kb mate pair.
As E. coli strains can differ quite a bit and we want to look at the differences between these strains both at genome (organizational) level and more local differences, I would guess that de novo assembly would be preferable if it can be done. Does anyone have experience with assembly of something like this? How is the quality of the genome compared to what you get with 454?
Cheers,
--
Einar Ryeng
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