Hi
We are considering to do a genome sequencing in one of our filamentous fungi, and would like to have some advices and hear your experiences on some off the different platforms.
The aim of the sequencing is to find a specific gene cluster involved in biosynthesis of an interesting compound.The fungi has an expected genome size of 30 Mb based on the closest related full genome sequenced fungi.
Of course the best option is some sort of hybrid strategy, however we don't at the moment have the budget for that. So instead we will just try and sequence on one platform.
So my questions is:
1. Which platform will you use for de novo sequencing of a 30 Mb filamentous fungi (at the moment GS-FLX and Illumina HiSeq seems as the best options with the HiSeq being the best and cheapest choice)
2. We had an offer for sequencing on the HiSeq. However the coverage was above 2000x making the price higher than we expected. How much coverage would you recommend as a minimum in this case?
3. For the assembly, does any of you have experience in the quality difference between assemblys done with CLC or for instance ABySS?
Any help would be appreciated.
Regards,
Kasper
We are considering to do a genome sequencing in one of our filamentous fungi, and would like to have some advices and hear your experiences on some off the different platforms.
The aim of the sequencing is to find a specific gene cluster involved in biosynthesis of an interesting compound.The fungi has an expected genome size of 30 Mb based on the closest related full genome sequenced fungi.
Of course the best option is some sort of hybrid strategy, however we don't at the moment have the budget for that. So instead we will just try and sequence on one platform.
So my questions is:
1. Which platform will you use for de novo sequencing of a 30 Mb filamentous fungi (at the moment GS-FLX and Illumina HiSeq seems as the best options with the HiSeq being the best and cheapest choice)
2. We had an offer for sequencing on the HiSeq. However the coverage was above 2000x making the price higher than we expected. How much coverage would you recommend as a minimum in this case?
3. For the assembly, does any of you have experience in the quality difference between assemblys done with CLC or for instance ABySS?
Any help would be appreciated.
Regards,
Kasper
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