| Time | Event | Session leader |
|---|---|---|
| 9:00 am – 9:30 am | Introduction - Welcome - Logging into NeSI |
Jian Sheng Boey |
| 9:30 am – 10:30 am | TASK: Bash scripting and introduction to Slurm scheduler | Dinindu Senanayake |
| 10:30 am – 10:50 am | Morning tea break | |
| 10:50 am – 11:10 am | TASK: Bash scripting (continued) | Dinindu Senanayake |
| 11:10 am – 11:40 pm | TALK: The metagenomics decision tree | Kim Handley |
| 11:40 am – 12:00 pm | DISCUSSION Guided discussions on approaches to metagenomics analyses | Kim Handley |
| 12:00 pm – 12:45 pm | Break for lunch (lunch not provided) | |
| 12:45 pm – 1:45 pm | TALK: Quality filtering raw reads TASK: Visualisation with FastQC TASK: Read trimming and adapter removal TASK: Diagnosing poor libraries TALK: Common issues and best practice TASK (Optional): Filtering out host DNA |
Annie West |
| 1:45 pm – 3:00 pm | TALK: Assembly - Choice of assemblers - Considerations for parameters, and when to stop! TASK: Prepare data for assembly TASK: Exploring assembler options TASK: Submitting jobs to NeSI via slurm TASK: Run SPAdes and IDBA-UD assembly TASK (Optional): Submitting variant assemblies to NeSI |
Kim Handley |
| 3:00 pm – 3:20 pm | Afternoon tea break (Tea, coffee, and snacks provided) | |
| 3:20 pm – 5:00 pm | TALK: Future considerations - co-assembly vs. single assemblies TASK: Assembly evaluation TASK: Short contig removal |
Jian Sheng Boey Kim Handley |
| Time | Event | Session leader |
|---|---|---|
| 9:00 am – 9:15 am | Introduction - Overview of yesterday, questions - Overview of today |
Annie West |
| 9:15 am – 9:30 am | RECORDED PRESENTATION: Genomic adaptations enabling Acidithiobacillus distribution across wide ranging hot spring temperatures and pHs (Chanenath Sriaporn) | Kim Handley |
| 9:30 am – 10:30 am | Binning (part 1) TALK: Overview of binning history - Key parameters and strategies for binning TASK: Read mapping |
Kim Handley |
| 10:30 am – 10:50 am | Morning tea break (Tea, coffee, and snacks provided) | |
| 10:50 am – 11:20 am | Binning (part 2) TASK: Multi-binning strategy (Metabat and Maxbin) |
Cesar Facimoto |
| 11:20 am – 12:00 pm | TALK: Overview of binning history (continued) - Key parameters and strategies for binning |
Kim Handley |
| 12:00 pm – 12:45 pm | Break for lunch (lunch not provided) | |
| 12:45 pm – 2:00 pm | Binning (part 3) TASK: Bin dereplication via DAS_Tool TASK: Evaluating bins using CheckM |
Cesar Facimoto |
| 2:00 pm - 2:30 pm | Binning (part 4) TALK: Discuss additional dereplication strategies, such as dRep TALK: How to work with viral and eukaryotic bins TALK: Dealing with organisms which possess minimal genomes |
Jian Sheng Boey Annie West |
| 2:30 pm - 3:00 pm | TALK: Bin refinement - Refinement strategies |
|
| 3:00 pm – 3:20 pm | Afternoon tea break (Tea, coffee, and snacks provided) | |
| 3:20 pm – 5:00 pm | TASK: Working with VizBin |
Jian Sheng Boey Annie West |
| Time | Event | Session leader |
|---|---|---|
| 9:00 am – 9:20 am | Introduction - Overview of yesterday, questions - Overview of today |
Jian Sheng Boey |
| 9:20 am – 10:30 am | TALK: Bin taxonomic classification - Bin and species determination TASK: Taxonomic classification using GTDB-Tk TASK: View phylogenetic trait distribution using ANNOTREE |
David Waite |
| 10:30 am – 10:50 am | Morning tea break (Tea, coffee, and snacks provided) | |
| 10:50 am – 12:00 pm | TALK: Identifying viruses from metagenomic data TASK: Identifying viral contigs using VIBRANT RECORDED PRESENTATION: Genetic exchange in ultra-small Patescibacteria (Emilie Gios) TASK: QC of viral contigs using CheckV TASK: Taxonomic classification of viruses using vContact2 |
Jian Sheng Boey Annie West |
| 12:00 pm – 12:45 pm | Break for lunch (lunch not provided) | |
| 12:45 pm - 1:30 pm | TALK: Gene prediction using prodigal and other tools (RNAmer, Aragorn, etc) TASK: Predict open reading frames and protein sequences |
Jian Sheng Boey Cesar Facimoto |
| 1:30 pm - 2:00 pm | TALK: Gene annotation (part 1) - Methods TASK: Gene annotation using DIAMOND and HMMER3 Discussion: Evaluating the quality of gene assignment |
Jian Sheng Boey Cesar Facimoto |
| 2:00 pm – 3:00 pm | TALK: Gene annotation (part 2) - Using online resources (e.g. KEGG, BioCyc, MetaCyc, HydDB, PSORT) TASK: View KEGG annotation in KEGG website |
Jian Sheng Boey Cesar Facimoto |
| 3:00 pm – 3:20 pm | Afternoon tea break | |
| 3:20 pm – 4:30 pm | TASK: MAG annotation with DRAM TASK: Coverage calculation using Bowtie2 TASK: Introduce group project goals TASK: Dividing into working groups / get a group name TASK: Select a goal from your project |
Annie West Kim Handley |
| 4:30 pm – 5:00 pm | End of day wrap up | Kim Handley |
| Time | Event | Session leader |
|---|---|---|
| 9:00 am – 9:15 am | Introduction - Overview of yesterday, questions - Overview of today |
Jian Sheng Boey |
| 9:15 am – 10:00 am | Presentation of data TALK: DRAM results overview TASK: Explore DRAM results |
Annie West |
| 10:00 am – 10:30 am | Presentation of data (genome distributions) TALK: Visualising findings (environmental distribution) TASK: Coverage heatmap and nMDS ordination |
Kim Handley |
| 10:30 am – 10:50 am | Morning tea break (Tea, coffee, and snacks provided) TASK: Workshop survey |
|
| 10:50 am – 12:00 pm | Presentation of data (metabolism) TALK: Visualising findings (metabolic maps, genome features, metabolic schematics, and gene trees) TASK: KEGG metabolic pathways TASK: Gene synteny TASK: CAZy heatmaps |
Cesar Facimoto Jian Sheng Boey |
| 12:00 pm – 12:45 pm | Break for lunch (lunch not provided) | |
| 12:45 pm – 2:30 pm | TASK: Analyse data for group work TASK: Prepare group presentation |
Kim Handley |
| 2:30 pm – 3:00 pm | Present and discuss findings TASK: Each group to give an informal presentation of their data |
Kim Handley |
| 3:00 pm – 3:20 pm | Afternoon tea break (Tea, coffee, and snacks provided) | |
| 3:20 pm – 3:40 pm | Present and discuss findings (continued) TASK: Each group to give an informal presentation of their data |
Annie West |
| 3:40 pm – 4:00 pm | End of day wrap up - Final discussion |
Kim Handley Jian Sheng Boey |