Applications of DNA sequencing Python Lab IV

##Goals

• Explore the various applications of DNA sequencing
• Introduce resequencing vs de novo assembly
• Build functions in python
• Write assertions in python

Concepts to Know

• Whole genome shotgun sequencing­ - general concept
• The basic steps in analysis of whole genome resequencing data
• Sequence capture ­ general idea, reasons you might want to do it instead of whole genome resequencing]
• What are some problems with targeted resequencing?
• RADSeq/ddRAD/GBS ­- what does each acronym stand for? What is reason to do these techniques instead of whole genome resequencing? What type of data are you trying to discover?
• What advantage does ddRAD have over GBS/RAD?
• Bisulfite sequencing ­- what is the purpose? How does it work? What problems often arise from bisulfite treatment
• Sequence assembly ­- what are some factors that increase difficulty
• Contig vs scaffold in assembly terms
• Steps of sequence assembly workflow
• What is N50 statistic?

##Materials

• Slides for Applications of DNA sequencing
• Finish up Python for Biologists Chapter 4 Lists and Loops
• Python for Biologists Chapter 5 Writing Our Own Functions

##HW HW4 = Due midnight on Wednesday, Sept 20th.