Metagenomics Summer School
Timetable 2023
Time |
Event |
Session leader |
---|---|---|
09:00 – 09:30 | Introductions Welcome Overview Login to NeSI via Jupyter Hub |
Jian Sheng Boey |
09:30 – 10:30 | TASK Bash scripting and Slurm scheduler I | Dinindu Senanayake |
10:30 – 10:50 | Morning tea | |
10:50 – 11:10 | TASK Bash scripting and Slurm scheduler II | Dinindu Senanayake |
11:10 – 11:45 | TALK Metagenomics decision tree | Kim Handley |
11:45 – 12:00 | TALK Project introduction and description | Kim Handley |
12:00 – 12:45 | Lunch | |
12:45 – 13:45 | Read QC TALK Quality filtering raw reads TASK Visualisation with FastQC TASK Read trimming & adapter removal TASK Diagnosing poor libraries TALK Common issues & best practices TASK (Optional) Filter out host DNA |
Annie West |
13:45 – 15:00 | Assembly TALK Choice of assemblers, parameter considerations, and when to stop! TASK Prepare data for assembly TASK Exploring assembler options TASK Submit assembly jobs to NeSI via Slurm TASK (Optional) Submit variant assembly jobs |
Kim Handley |
15:00 – 15:20 | Afternoon tea | |
15:20 – 17:00 | Assembly TALK Future considerations: co-assembly vs. single assemblies TASK Assembly evaluation TASK Short contig removal |
Mike Hoggard |
Time |
Event |
Session leader |
---|---|---|
09:00 – 09:15 | Introductions Recap of day 1 Overview of the day |
Annie West |
09:15 – 10:15 | Binning I TALK Overview of binning history, key parameters, and strategies I TASK Read mapping |
Kim Handley |
10:15 – 10:45 | Binning II TASK Multi-binning strategy with MetaBat and MaxBin |
Mike Hoggard |
10:45 – 11:00 | Morning tea | |
11:00 – 11:40 | Binning II (continued) TALK Overview of binning history, key parameters, and strategies II |
Kim Handley |
11:40 – 12:00 | DISCUSSION Binning strategies TASK Compare and contrast outputs of binning tools |
Annie West |
12:00 – 12:45 | Lunch | |
12:45 – 14:00 | Binning III TASK Bin dereplication using DAS_Tool TASK Evaluate bins using CheckM |
Kim Handley |
14:00 – 14:30 | Binning IV TALK Additional dereplication strategies such as dRep TALK Working with viral and eukaryotic bins TALK Organisms possessing minimal genomes |
Mike Hoggard Kim Handley |
14:30 – 15:00 | TALK Bin refinement: Strategies | Mike Hoggard Kim Handley |
15:00 – 15:20 | Afternoon tea | |
15:20 – 16:00 | TASK Bin refinement: VizBin | Jian Sheng Boey Mike Hoggard |
16:00 – 16:15 | PRESENTATION Emilie Gios - Genetic exchange in ultra-small Patescibacteria | Kim Handley |
16:15 – 17:00 | Wrap up TASK Submit jobs for VirSorter2 and CheckV Summary of the day |
Mike Hoggard Kim Handley |
Time |
Event |
Session leader |
---|---|---|
09:00 – 09:20 | Introductions Recap of day 2 Recap of binning outputs Overview of the day |
Jian Sheng Boey |
09:20 – 10:30 | Taxonomic annotation of prokaryotic bins TALK Taxonomic classification: Bin and species determination TASK Taxonomic classification using GTDB-Tk TASK View phylogenetic trait distribution using ANNOTREE |
David Waite |
10:30 – 10:50 | Morning tea | |
10:50 – 11:20 | Phylogenomics TALK Primer to phylogenetic analyses TASK Build a phylogenetic tree using FASTTREE TASK Visualise tree using iTOL |
Valter Almeida |
11:20 – 12:00 | Viruses TALK Identifying viruses from metagenomic data TASK Identify viral contigs using VirSorter2 TASK QC of viral contigs using CheckV TALK Predicting viral taxonomy using vConTACT2 TASK (Optional) Visualise vConTACT2 viral gene sharing network in Cytoscape |
Mike Hoggard |
12:00 – 12:45 | Lunch | |
12:45 – 13:30 | Gene prediction TALK Tools for predicting genes: Prodigal, RNAmer, Aragorn, etc. TASK Predict ORFs and protein sequences using Prodigal |
David Waite |
13:30 – 14:00 | Gene annotation I TALK Primer on annotation method TASK Annotate predicted genes using DIAMOND and HMMER3 DISCUSSION Evaluate the quality of gene assignments |
Jian Sheng Boey |
14:00 – 15:00 | Gene annotation II TALK Using online resources (KEGG, BioCyc, MetaCyc, HydDB, PSORT) TASK View KEGG annotations online |
Jian Sheng Boey |
15:00 – 15:20 | Afternoon tea | |
15:20 – 15:35 | PRESENTATION Kitty Sriaporn - Genomic adaptations enabling Acidithiobacillus distribution across wide-ranging hot spring temperatures and pHs | Kim Handley |
15:35 – 16:15 | Gene annotation III TASK MAG annotation with DRAM TASK Coverage calculation using Bowtie2 |
Annie West Mike Hoggard |
16:15 – 16:30 | Group project TASK Group formation TASK Topic selection |
Kim Handley |
16:30 – 17:00 | Wrap up Summary of the day |
Jian Sheng Boey |
Time |
Event |
Session leader |
---|---|---|
09:00 – 09:15 | Introductions Recap of day 3 Overview of the day |
Jian Sheng Boey |
09:15 – 10:00 | DRAM outputs TALK Overview of DRAM results TASK Explore DRAM results |
Annie West |
10:00 – 10:30 | Environmental distribution TALK Visualising findings TASK Coverage heatmap and nMDS ordination |
Mike Hoggard |
10:30 – 10:50 | Morning tea | |
10:50 – 11:00 | TASK Workshop survey | |
11:00 – 12:00 | Genomic features and metabolism TALK Visualising findings TASK KEGG metabolic maps TASK Gene synteny |
Jian Sheng Boey Annie West |
12:00 – 12:45 | Lunch | |
12:45 – 14:30 | Group work TASK Analyse data TASK Prepare presentations |
Kim Handley Mike Hoggard David Waite |
14:30 – 15:00 | Group work TASK Informal group presentations |
Kim Handley Mike Hoggard David Waite |
15:00 – 15:20 | Afternoon tea | |
15:20 – 15:40 | Group work TASK Informal group presentations |
Kim Handley Mike Hoggard David Waite |
15:40 – 16:00 | Wrap up Final discussions |
Appendices
License
Genomics Aotearoa / New Zealand eScience Infrastructure / University of Auckland Metagenomics Summer School material is licensed under the GNU General Public License v3.0, 29 June 2007. (Follow this link for more information)
Slides for workshop
You can find a copy of the slides presented during the workshop, with published figures removed, in the slides/ folder.
Snapshots of results to download
If you are having trouble downloading files using scp
, we are providing exemplar output files, which you can download through your browser, here, or via the following links:
Post-workshop survey
Thank you for attending Metagenomics Summer School 2023! We would like your feedback on how we have done and what we can improve on. You can provide feedback here.