Technology Experimental Design Cost Estimation

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Presentation transcript:

Technology Experimental Design Cost Estimation Pacific Biosciences Technology Experimental Design Cost Estimation

Pac Bio Systems RSII System Sequel System

Pac Bio Systems RSII SEQUEL 150K ZMWs per SMRT Cell Fasta file output 1M ZMWs per SMRT Cell 6.5x more throughput 3x more expensive/SMRT cell Potential range in SMRT cell sizes Potential increase in library efficiency Bam output Length differential is currently significant, such that cost/base is about parity

Pacific Biosciences Libraries Structurally linear Topologically circular Structural homogeneity of templates Provides sequences of both forward and reverse strands in the same trace. Input recommends 15ug of DNA per library

Estimating Costs (UC Pricing) Cost of extracting high-molecular weight DNA Performed within the lab, or by a third-party vendor such as Amplicon Express Library Preparation [ @ $470/library] Blue Pippen size selection [ @ $142/2-libraries ] First SMRT cell (calibrate loading) [ @ $429 ] Remaining SMRT cells [ @ $383/SMRT, 10 SMRT cells per library ] Bioinformatic Assembly [ 40 hours @ $97/hour ] Use an estimate of 1Gb/SMRT cell and target > 65x coverage for a goal of > 30x coverage of > 10Kb reads. http://dnatech.genomecenter.ucdavis.edu/prices/

Cost estimation exercises Cost of a 200Mb Genome? Cost of a 1Gb Genome? Cost of human sized 3Gb Genome? Cost of crazy salamander 15Gb genome?

Cost of human sized 3Gb Genome? Cost of a 200Mb Genome? 200Mb * 65x = 13Gb = 13 SMRT Cells, Means 2 Libraries, 1 Pippen 383*12+429*1+142*1+470*1+40*97 = $9,517 Cost of a 1Gb Genome? 1Gb * 65x = 65Gb = 65 SMRT Cells, Means 7 Libraries, 4 Pippen 383*65+429*1+142*4+470*7+40*97 = $33,062 Cost of human sized 3Gb Genome? 3GB * 65x = 195Gb = 195 SMRT Cells, Means 20 Libraries, 10 Pippen 383*195+429*1+142*10+470*20+40*97 = $89,814 Cost of crazy salamander 15Gb genome? 15GB * 65x = 975Gb= 975 SMRT Cells, Means 98 Libraries, 44 Pippen 383*975+429*1+142*98+470*44+40*97 = $ 412,330