Contact the GHTF to schedule a consultation about experimental design. Below are a number of commonly asked questions to help you begin planning your experiment. Please consult with us to let us know the time frame of your experiment and to give you an idea of our current workload.
How to calculate expected coverage from a next gen sequencing experiment.
Currently a good library will give 180 to 200 million reads per lane on the HiSeq 2500 with the version 3 chemistry and 320-380 million reads on the HiSeq 4000. Thus to calculate expected coverage you multiply the number of reads by the number of cycles run. For example, if a paired end 100 cycle run is done the expected number of reads is 100,000,000 reads x 100 cycles x 2 ends = 20,000,000,000 or 20 GB
Suggestions for making next gen sequencing libraries
GHTF has experience with kits from BiooScientific, Kapa Biosciences, ZymoResearch, NuGen, Clontech Takara and Illumina. Commercial kits are changing rapidly towards reducing the protocol time and allowing lower inputs of sample. We are available to discuss the protocols that will be optimal for your experimental design and goals. For whole exome libraries, the Agilent, Roche (Nimblegen) and Illumina TruSeq all work well.