Andrew Severin

Andrew Severin

His PhD was in Biophysics/NMR spectroscopy. He did a Bioinformatics Postdoc in Soybean genetics and now runs the Genome Informatics Facility at Iowa State University. He is passionate about evolution and the science behind the genome. There is so much we don't know about how the elements in a genome interact to create the fine balance of gene expression, modification and 3D structure that create the dynamic range of phenotypes we observe. As sequencing technology continues to improve and the cost continues to decrease, we will be able to ask more complex questions that increase our understanding via comparative and translational genomics.

Sex Determination in a Fish

Background

Aquaculture production has become increasingly important to satisfy seafood and fishery product demands. Researcher wants to develop genomic resources to improve sustainable domestic aquaculture. They recently assembled and annotated a genome and now want to collect wild fish to explore genetic diversity in local populations and identify the sex determining region.

Ideal Experimental Design Elements

  • Funding for project $X,XXX
  • Sequencing Technology: Illumina HiSeq 3000
  • Number of lanes: 20 lanes
  • Length of read: 150bp
  • Number of Samples: 90
  • Coverage Depth: 29x
  • Year of Sequencing: hypothetical 2017

Real Experimental Design Elements

  • Funding for project $X,XXX
  • Sequencing Technology: Illumina HiSeq 2500
  • Number of lanes: 4 lanes
  • Length of read: 100bp
  • Number of Samples: 90
  • Coverage Depth: 1.9x
  • Year of Sequencing: 2015

Questions

How is Coverage Depth Determined?

The quick and dirty calculation is to take the read length (150) multiply by 2 if it is paired end multiply by the number of fragments the Illumina machine produces (300 Million) = 150bp * 2 * 300M = 90,000 million or 90 billion bases output from a single lane. Take that number and divide it by your genome size. If your genome size is 1 gigabase then you have approximately 90x coverage.

While this can give an approximation for coverage depth the reality is that the coverage depth at any given locus in the genome will be a distribution around this number with some regions having more and some regions having less coverage.

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