Only three persons presented their work

• Eda
• Faruk
• Atakan

• Ayşe Nur
• Buşra
• Esra

You don’t need to make it perfect

Incomplete results show how you work

The idea is to make a practical work based on the first part of the course (assembly)

If necessary we can also make theoretical questions about the second part (alignment)

Oppegaard, H, T M Steinum, and Y Wasteson. “Horizontal Transfer of a Multi-Drug Resistance Plasmid between Coliform Bacteria of Human and Bovine Origin in a Farm Environment.” Applied and Environmental Microbiology 67, no. 8 (2001): 3732–34. doi:10.1128/AEM.67.8.3732-3734.2001. https://aem.asm.org/content/aem/67/8/3732.full.pdf

The data is in our server (rstudio.iu.edu.tr), on the folder /home/bioinfo.

The idea is to follow a standard workflow, similar to Kaan’s presentation

“WGS/WES Mapping to Variant Calls”: http://www.htslib.org/workflow/

(only the first part)

• Work in groups of two people
• There are two NGS libraries: F5 and F20
• Each group focus on a single library
• Each library has a reference genome
• There is also a reference plasmid

• Map the reads to the genome and plasmid
  • Which reads map on the genome, the plasmid, both or none?
• Find variants according to the protocol
• Write a report of them
  • How many?
  • What kind of variant?
  • Where?
• Bonus question
  • Can you identify the genes where the reads map?