Genome Bioinformatics - Computer practicals

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

Schedule Computer practicals Genome Bioinformatics

  1. Wednesday (April 23rd), 13:15 - 17:00: COOI (Daniel)
  2. Friday (April 25th), 11:00 - 15:00: COOII (Daniel)
  3. Wednesday (April 30th), 11:00 - 15:00: COOIII (Daniel)
  4. Friday (May 2nd), 11:00 - 15:00: COOI (Berend)
  5. Wednesday (May 7th), 11:00 - 15:00: COOII (Berend)
  6. Friday (May 9th), 11:00 - 15:00: COOIII (Berend)
  7. Wednesday (May 14th), 11:00 - 15:00: COOI (Michael)
  8. Friday (May 16th), 11:00 - 15:00: COOII (Michael)
  9. Wednesday (May 21th), 11:00 - 15:00: COOIII (Michael)

A cheat sheet of the used Linux commands is available.

Schedule

Setup Download tools, if needed, required for the lessons
Day 1 00:00 1. Block 1 - COOI: Recovering a microbial community What interesting microbes can we find around us?
00:20 2. COO-I-1. Sequencing How to obtain metagenomic sequencing data?
00:45 3. COO-I-2. Data processing How to assess the quality of the sequencing reads?
01:15 4. COO-I-3. Metagenome assembly How to assemble metagenomes from sequencing reads?
02:15 5. COO-I-4. Binning How to cluster contigs into bins in a metagenomic assembly?
03:15 Finish
Day 2 00:00 6. Block 1 - COOII: Reconstructing evolutionary history How can we establish the identity of novel Metagenome-Assembled Genomes?
00:00 7. COO-II-1. Genome annotation How to annotate genomes?
00:30 8. COO-II-2. 16S rRNA phylogenetics How to identify the taxonomy of an organism based on a common phylogenetic marker?
01:45 9. COO-II-3. Phylogenomic reconstruction How to use whole-genome information to place an organism in the tree of life?
03:00 Finish
Day 3 00:00 10. Block 1 - COOIII: A hot take on evolution How can we identify genomic adaptations to new niches?
00:00 11. COO-III-1. Growth parameter prediction How to use genome features to predict growth parameters?
00:40 12. COO-III-2. Genome architectural features related to niche adaptation How do genomes evolve under different environmental constraints?
01:25 13. COO-III-3. Gene content associated with niche adaptation How do genomes evolve under different environmental constraints?
02:35 14. COO-III-4. Genome composition and optimal growth temperature How do genomes evolve under different environmental constraints?
03:05 Finish
Day 4 00:00 15. Block 2 - COOI: Gene tree intepretation & orthology of an important metabolic enzyme How is my human gene related to genes in other model organisms and what does this tell me about orthologs
00.75:45.0 16. Block 2 - COOI Manually interpreting a more complicated gene tree What is the evolutionary history of the RasGEF gene family in animals, fungi and the slime mold
01.5:30.0 17. Block 2 -Using NOTUNG for tree reconciliation Can we better understand tree reconciliation by doing it also using a program
02.0:00.0 18. Block 2 - COOI putting it all together on the species tree Can we project the events from the annotated RasGEF tree onto the species tree
02.5:30.0 Finish
Day 5 00:00 19. Block 2 - COOII: Making our own orthologs between animals and plotting their conservation how well (on average) are two orthologs between two species conserved?
03.0:00.0 20. Block 2 - COOII: Making our own orthologs between animals and plotting their conservation: code answers how well (on average) are two orthologs between two species conserved?
03.0:00.0 Finish
Day 6 00:00 21. Block 2 - COOIII: Horizontal gene transfer in a gene tree of an aminoacyl-tRNA synthetase Can we recognize HGT in a gene tree?
01.0:00.0 22. Block 2 - COOIII: Profile searches What is actually happening during an iterative profile search?
01.75:45.0 23. Block 2 - COOIII: size of a gene family Can we quickly establish the size of a gene family in a predicted proteome?
02.25:15.0 Finish

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