Microbial Genomics - computer practical

This lesson uses the Software Carpentry and Data Carpentry lesson template.

Schedule computer practical

  1. Wednesday, 10:00 - 10:45: Intro lecture genome assembly quality
  2. Wednesday, 10:45 - 10:55: Intro
  3. Wednesday, 10:55 - 11:15: Genome assemblies
  4. Wednesday, 11:15 - 12:00: Genome assembly assessment and comparision with Quast
  5. Wednesday, 12:00 - 12:30: Gemome completness with BUSCO
  6. Wednesday, 13:15 - 15:30: Whole-genome alignmnet with MUMMER
  7. Wednesday, 15:30 - … : Discussion
  8. Monday, 09:00 - 10:00: Intro lecture into pan-genomes
  9. Monday, 10:00 - 11:30: How to build a pan-genome graphs
  10. Monday, 11:30 - 12:45: Genome partitioning
  11. Monday, 13:15 - 15:30: Pan-genome graphs for fungal genomes
  12. Monday, 15:30 - … : Discussion

Data

This computer practical uses data from this publication and from jgi. A cheat sheet of the used Linux commands is available.

Schedule

Setup Download files required for the lesson
00:00 1. Introduction What type of data do we work on?
How does the genome of Zymoseptoria tritici look like?
00:10 2. Genome assembly information How can you obtain and interpret genome assembly information from NCBI?
00:30 3. Genome assembly quality How can we interpret the genome assembly quality of fungal genome assemblies?
01:15 4. Genome assembly completness How can we assess completness of fungal genome assemblies?
01:45 5. Genome comparisons How can we compare two genome assemblies?
How can we interpret whole-genome alignments to identify large-scale genomic differences?
04:00 6. Introduction to pan-genome graphs How can we build a pan-genome graph of multiple sequences?
How can we interpret the basic features of a pan-genome graph?
05:30 7. Genome partitioning How can we identify homologous chromosomes between individuals/strains?
How can we interpret the similarity between chromosomes and related these to biology?
06:30 8. Pan-genome graphs of Zymoseptoria tritici How can we build a pan-genome graph for individual communities?
How can we interpret the more complex pan-genome graphs?
How can we relate features of the pan-genome graph to pair-wise genome comparisons?
09:00 Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.