Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in December.
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.
- Bash scripting
- The metagenomics decision tree
- Quality filtering raw reads
- Assembly
- Evaluating the overnight assembly
- Overview of binning history
- Binning (part 1, initial binning)
- Binning (part 2, dereplication)
- Binning (part 3)
- Gene annotation (refresher)
- Presentation of data
| Time | Event |
|---|---|
| 9:00 am – 9:45 am | Introduction Welcome Logging into NeSI |
| 9:45 am – 10:30 am | Bash scripting |
| 10:30 am – 10:50 am | Morning tea break |
| 10:50 am – 11:30 am | Bash scripting (continued) |
| 11:30 am – 12:00 pm | The metagenomics decision tree Proposing a hypothesis for your project Dividing into working groups |
| 12:00 pm – 12:45 pm | Break for lunch |
| 12:45 pm – 1:45 pm | Quality filtering raw reads Visualisation with FastQC Read trimming and adapter removal Diagnosing poor libraries Common issues and best practice |
| 1:45 pm – 3:00 pm | Assembly Choice of assemblers Considerations for parameters, and when to stop! |
| 3:00 pm – 3:20 pm | Afternoon tea break |
| 3:20 pm – 3:45 pm | Assembly (continued) Submitting jobs to NeSI via slurm |
| 4:00 pm – 5:00 pm | End of day wrap up Attendees can work with their own data, if available |
| Time | Event |
|---|---|
| 9:00 am – 9:30 am | Introduction Overview of yesterday, questions Overview of today |
| 9:30 am – 10:30 am | Evaluating the overnight assembly Future considerations – co-assembly vs single assemblies Run evaluation tool/script |
| 10:30 am – 10:50 am | Morning tea break |
| 10:50 am – 12:00 pm | Overview of binning history ESOM, differetial coverage, tetranucleotide frequencies Strategies for binning |
| 12:00 pm – 12:45 pm | Break for lunch |
| 12:45 pm – 1:45 pm | Binning (part 1) Short contig removal Read mapping Multi-binning strategy (Metabat and Maxbin) |
| 1:45 pm – 3:00 pm | Binning (part 2) Bin dereplication via DAS_Tool Evaluating bins using CheckM |
| 3:00 pm – 3:20 pm | Afternoon tea break |
| 3:20 pm – 4:00 pm | Binning (part 3) Discuss additional dereplication strategies, such as dRep How to work with viral and eukaryotic bins Dealing with organisms which possess minimal genomes |
| 4:00 pm – 5:00 pm | End of day wrap up Attendees can work with their own data, if available |
| Time | Event |
|---|---|
| 9:00 am – 9:30 am | Introduction Overview of yesterday, questions Overview of today |
| 9:30 am – 11:30 am | Bin refinement Working with VizBin (hands on) Other strategies (ESOMana) |
| 10:30 am – 10:50 am | Morning tea break |
| 10:50 am – 11:30 am | Gene prediction Introduce prodigal, discuss single vs meta mode Discuss what prodigal can't find, discuss other tools (RNAmer, Aragorn, etc) |
| 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) |
| 12:00 pm – 12:45 pm | Break for lunch |
| 12:45 pm – 3:00 pm | Gene annotation (part 2)) Overview of the BLAST XML output Looking at gene networks in MEGAN Tie findings to your initial hypothesis |
| 3:00 pm – 3:20 pm | Afternoon tea break |
| 3:20 pm – 4:00 pm | Gene annotation (continued) Using online resources (KEGG, BioCyc, MetaCyc, HydDB, PSORT) Tie findings to your initial hypothesis |
| 4:00 pm – 5:00 pm | End of day wrap up Attendees can work with their own data, if available |
| Time | Event |
|---|---|
| 9:00 am – 9:30 am | Introduction Overview of yesterday, questions Overview of today |
| 9:30 am – 10:30 am | Gene annotation (refresher) Tie findings to your initial hypothesis |
| 10:30 am – 10:50 am | Morning tea break Fill in form on hypothesis for own work |
| 10:50 am – 12:00 pm | Present and discuss findings Each group to give a casual discussion of their data What they were looking for, what did they find? Which databases were most helpful? |
| 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* Gene synteny alignments (R) |
| 3:00 pm – 3:20 pm | Afternoon tea break |
| 3:20 pm – 4:00 pm | End of day wrap up Final discussion |