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Old 09-14-2017, 10:45 PM   #2
Genetic Librarian
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Location: Europe

Join Date: May 2017
Posts: 31
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Hi,

Question 1: Your output requirement is 16kb (target size) * 3000 (coverage)

Thus, per sample you would need 48 Megabases as output.
A MiSeq v2 2x 150 bp PE run e.g. has an output of 5 Gigabases, so theoretically you could pool 104 samples on one Run. Substract a bit of duplicates, unassigned samples, PhiX etc. and you could aim for ~80 samples / Run.
Basically, that is what the Illumina Coverage Calculator does .

You can calculate the number of samples on a HiSeq lane (Output 90 Gb / Lane) yourself (hint: this is absolute overkill vor mtGenomes).

Question 2: For mtGenome, we used the Nextera XT Kit with its associated Indices.
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