Hi all
I'm planning a project to sequence multiple bacterial strains and am trying to calculate how many samples I can multiplex per lane while getting sufficient coverage to accurately determine polymorphisms. According to the VAAL paper from the Broad (http://www.nature.com/nmeth/journal/...meth.1286.html), 1 lane of 36 bp reads for Staph aureus gave ~53x Q20 coverage (table S1). I calculate that this is about 64% of the total sequence produced for the lane. I haven't come across any other similar calculations in the literature. What is your experience with the total amount of sequencing needed to ensure 20-30x Q20 coverage?
I'm planning a project to sequence multiple bacterial strains and am trying to calculate how many samples I can multiplex per lane while getting sufficient coverage to accurately determine polymorphisms. According to the VAAL paper from the Broad (http://www.nature.com/nmeth/journal/...meth.1286.html), 1 lane of 36 bp reads for Staph aureus gave ~53x Q20 coverage (table S1). I calculate that this is about 64% of the total sequence produced for the lane. I haven't come across any other similar calculations in the literature. What is your experience with the total amount of sequencing needed to ensure 20-30x Q20 coverage?
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