Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in November.
A draft timetable for the day is provided below, but please keep in mind that this is subject to change as we evaluate our course material.
For all exercises after the bash introduction, you will be working from the file path
/nesi/nobackup/nesi02659/MGSS_U/YOUR_USERNAME/A few helpful commands and shortcuts for working in bash or with slurm can be found here.
If you are having trouble downloading files using scp, we are providing exemplar output files which you can download through your browser, here.
You can find a copy of the slides presented during the workshop, with published figures removed, in the slides/ folder.
You can find a saved version of the workshop Etherpad notes here.
- Evaluating the overnight assembly
- Binning (part 1, read mapping)
- Binning (part 2, initial binning)
- Binning (part 3, dereplication)
- Bin refinement
- Viruses
- Coverage and Taxonomy
- Gene prediction
- Gene annotation (part 1)
- Gene annotation (part 2)
| Time | Event | Session leader |
|---|---|---|
| 9:00 am – 9:45 am | Introduction Welcome Logging into NeSI |
David Waite |
| 9:45 am – 10:30 am | TASK: Bash scripting | Dinindu Senanayake Ngoni Faya |
| 10:30 am – 10:50 am | Morning tea break | |
| 10:50 am – 11:30 am | TASK: Bash scripting (continued) | Dinindu Senanayake Ngoni Faya |
| 11:30 am – 12:00 pm | The metagenomics decision tree TASK: Dividing into working groups TASK: Select a goal for your project |
Kim Handley |
| 12:00 pm – 12:45 pm | Break for lunch | |
| 12:45 pm – 1:45 pm | Quality filtering raw reads TASK: Visualisation with FastQC TASK: Read trimming and adapter removal Diagnosing poor libraries Common issues and best practice |
Florian Pichlmuller |
| 1:45 pm – 3:00 pm | Assembly (part 1) Choice of assemblers Considerations for parameters, and when to stop! TASK: Exploring assembler options TASK: Submitting jobs to NeSI via slurm |
David Waite |
| 3:00 pm – 3:20 pm | Afternoon tea break | |
| 3:20 pm – 3:45 pm | Assembly (part 2) TASK: Submitting variant assemblies to NeSI |
David Waite |
| 4:00 pm – 5:00 pm | End of day wrap up Attendees can work with their own data, if available |
Kim Handley David Waite |
| Time | Event | Session leader |
|---|---|---|
| 9:00 am – 9:30 am | Introduction Overview of yesterday, questions |
Kim Handley |
| 9:30 am – 10:30 am | Evaluating the overnight assembly TASK: Run evaluation tool/script |
Kim Handley |
| 10:30 am – 10:50 am | Morning tea break | |
| 10:50 am – 11:20 am | Overview of binning history | Kim Handley |
| 11:20 am – 12:00 pm | Binning (part 1) TASK: Short contig removal TASK: Read mapping |
Kim Handley |
| 12:00 pm – 12:45 pm | Break for lunch | |
| 12:45 pm – 1:15 pm | Overview of binning history (continued) Key parameters and strategies for binning |
Kim Handley |
| 1:15 pm – 1:45 pm | Binning (part 2) TASK: Multi-binning strategy |
Kim Handley |
| 1:45 pm - 3:00 pm | Binning (part 3) TASK: Bin dereplication via DAS_Tool TASK: Evaluating bins using CheckM |
Kim Handley |
| 3:00 pm – 3:20 pm | Afternoon tea break | |
| 3:20 pm – 4:00 pm | Binning (part 4) Discuss additional dereplication strategies, such as dRep How to work with viral and eukaryotic bins Dealing with organisms which possess minimal genomes |
Kim Handley David Waite |
| 4:00 pm – 5:00 pm | End of day wrap up Optional: View assemblies with TAblet Attendees can work with their own data, if available |
Kim Handley David Waite |
| Time | Event | Session leader |
|---|---|---|
| 9:00 am – 9:30 am | Introduction Overview of yesterday, questions Overview of today |
David Waite |
| 9:30 am – 10:30 am | Bin refinement Refinement strategies - VizBin and ESOMana TASK: Working with VizBin TASK: Bin taxonomy with GTDB-TK |
David Waite |
| 10:30 am – 10:50 am | Morning tea break | |
| 10:50 am – 11:30 am | Gene prediction Introduce prodigal, discuss single vs anon mode Discuss what prodigal can't find, and where other tools are needed (RNAmer, Aragorn, etc)TASK: Predicting genes with prodigal and FragGeneScan |
Christina Straub |
| 11:30 am – 12:00 pm | Gene annotation (part 1) BLAST-like gene annotation using usearch or diamond Introduce the different databases, highlight our reasons for KEGG Evaluating the quality of gene assignment Differences in taxonomies (GTDB, NCBI etc) |
David Waite |
| 12:00 pm – 12:45 pm | Break for lunch | |
| 12:45 pm – 3:00 pm | Gene annotation (part 2)) TASK: Performing annotation with diamond TASK: Examining gene networks in MEGAN TASK: Tie findings to your initial goal |
David Waite |
| 3:00 pm – 3:20 pm | Afternoon tea break | |
| 3:20 pm – 4:00 pm | Gene annotation Using online resources (KEGG, BioCyc, MetaCyc, HydDB, PSORT) TASK: Tie findings to your initial hypothesis |
Kim Handley |
| 4:00 pm – 5:00 pm | End of day wrap up Attendees can work with their own data, if available |
Kim Handley David Waite |
| Time | Event | Session leader |
|---|---|---|
| 9:00 am – 9:30 am | Introduction Overview of yesterday, questions Overview of today |
Kim Handley |
| 9:30 am – 10:30 am | Gene annotation (refresher) TASK: Tie findings to your initial goal TASK: Prepare group presentation |
Kim Handley |
| 10:30 am – 10:50 am | Morning tea break TASK: Survey |
|
| 10:50 am – 12:00 pm | Present and discuss findings TASK: Each group to give a casual discussion of their data* What were you looking for, what did you find? Which databases were most helpful? |
Kim Handley |
| 12:00 pm – 12:45 pm | Break for lunch | |
| 12:45 pm – 3:00 pm | Presentation of data How do visualise findings - Metabolism maps, heatmaps, gene trees* TASK: Gene synteny alignments and heatmaps |
David Waite |
| 3:00 pm – 3:20 pm | Afternoon tea break | |
| 3:20 pm – 4:00 pm | End of day wrap up Final discussion |
Kim Handley David Waite |