9/12/2014
Customer asks for cost estimate and configuration for sequencing a non-model organism's genome; a reference genome is unavailable. Genome size is estimated to be ~1Gbp. Illumina platform is to be used.
Fri, 09/12/2014 at 11:29 AM
AccuraScience LB: For a 1G bp genome, achieving 100X coverage (generally required for a successful assembly of the genome) would take 1E11 bases of sequencing. If we plug in the common setting of similar applications - 100bp pair-ended reads, it will require 1 billion reads, corresponding to ~5 lanes of Illumina's Hiseq runs. If each lane costs $3500 to sequence, the sequencing cost would be ~$17.5K.
Besides sequencing cost, anther portion of the experimental cost is library preparation. I would recommend at least 2 libraries, the first at 45X coverage with 180bp fragment size, and the second at 45X coverage, using 3Kb short-jump library. If your budget allows, a third, 6Kb long-jump library at 5X coverage or even a shadow 40Kb fosmid-jump library would likely help.
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