This course is given at Navet (E10:1307) at BMC.
Instructors:
Course Assistants:
Please note this timetable is approximate and subject to change.
| Time | Activity |
|---|---|
| Day 1 | |
| 09.00 - 09.15 | Introduction |
| 09.15 - 10.00 | Session 1: Getting started in Genome Assembly |
| 10.00 - 10.15 | Coffee break / fika |
| 10.15 - 10.45 | Session 1 Exercises |
| 10.45 - 11.15 | Session 2: Sequence Data Quality Assessment - Corruption, Coverage, and Subsampling |
| 11.15 - 12.00 | Session 2 Exercises |
| 12.00 - 13.00 | Lunch |
| 13.00 - 13.45 | Session 3: Sequence Data Quality Assessment - FastQC, Contamination, Trimming, Duplication, and filtering |
| 13.45 - 15.00 | Session 3 Exercises |
| 15.00 - 15.15 | Coffee break / fika |
| 15.15 - 16.00 | Session 4: Sequence Data Quality Assessment - Kmer Analysis using KAT |
| 16.00 - 17.00 | Session 4 Exercises |
| Day 2 | |
| 09.00 - 09.30 | Discussion of previous days exercises |
| 09.30 - 10.00 | Session 5: Overview of de novo assembler principles |
| 10.00 - 10.15 | Coffee break / fika |
| 10.15 - 10.45 | Session 6: Assembly Validation - Assembly Statistics, and misassembly detection |
| 10.45 - 12.00 | Session 6 Exercises |
| 12.00 - 13.00 | Lunch |
| 13.00 - 13.30 | Session 7: Assembly Validation - Assembly Graphs and contamination detection |
| 13.30 - 15.00 | Session 7 Exercises |
| 15.00 - 15.15 | Coffee break / fika |
| 15.15 - 15.45 | Session 8: Assembly Validation - Gene space statistics and comparitive alignment |
| 15.45 - 17.00 | Session 8 Exercises |
| Day 3 | |
| 09.00 - 9.30 | Discussion of previous days exercises |
| 09.30 - 10.00 | Session 9: Small genome Assembly |
| 10.00 - 10.15 | Coffee break / fika |
| 10.15 - 12.00 | Session 9 Exercises |
| 12.00 - 13.00 | Lunch |
| 13.00 - 13.30 | Session 10: Challenges in assembly |
| 13.30 - 15.00 | Session 10 Exercises |
| 15.00 - 15.15 | Coffee break / fika |
| 15.15 - 17.00 | Session 11: Group Discussion and Summary |