Metagenomics Summer School¶

Day	Lesson topic
Day 1: Assembly	1. (Pre-Summer School) Introduction I: Shell 2. (Pre-Summer School) Introduction II: HPC and job scheduler 3. Filter raw reads by quality 4. Assembly I: Assembling contigs 5. Assembly II: Variable parameters 6. Assembly evaluation
Day 2: Binning	1. Introduction to binning 2. Binning with multiple tools 3. Bin dereplication 4. Manual bin refinement 3. Identifying viral contigs in metagenomic data
Day 3: Annotation	1. Assigning taxonomy to refined prokaryotic bins 2. Phylogenomics 3. Virus taxonomy 4. Gene prediction 5. Gene annotation I: BLAST-like and HMM 6. Gene annotation II: DRAM and coverage calculation
Day 4: Visualisation	1. Gene annotation III: DRAM distillation 2. Introduction to data presentation 3. Coverage heatmaps 4. Ordinations 5. KEGG pathway maps 6. Gene synteny 7. CAZy heatmaps

Timetable 2024¶

Day 1: Tuesday, 3^rd SepDay 2: Wednesday, 4^th SepDay 3: Thursday, 5^th SepDay 4: Friday, 6^th Sep

Time	Event	Session leader
09:00 – 09:25	Introductions Welcome Overview Login to NeSI via Jupyter Hub and test script	Jian Sheng Boey
09:25 – 09:55	TALK Metagenomics decision tree DISCUSSION What are your research questions?	Kim Handley
09:55 – 10:30	Read QC TALK Quality filtering raw reads TASK Visualisation with FastQC and MultiQC	Annie West
10:30 – 10:50	Morning tea
10:50 – 11:25	TASK Read trimming & adapter removal TASK Diagnosing poor libraries TALK Common issues & best practices TASK Filter out host DNA	Annie West
11:25 – 12:30	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 Submit variant assembly jobs	Kim Handley
12:30 – 13:30	Lunch
13:30 – 14:15	TALK Other considerations: assembly strategies TALK Assembly evaluation TASK Evaluate your assemblies TASK Short contig removal	Mike Hoggard
14:15 – 15:00	TALK Other considerations: rRNA reconstruction TASK Ribosomal RNA reconstruction using PhyloFlash TALK Other considerations: read classification	Annie West Jian Sheng Boey
15:00 – 15:20	Afternoon tea
15:20 – 15:50	TASK Sequence classification using Kraken2 and Bracken	Annie West Jian Sheng Boey
15:50 – 16:00	TALK Project introduction and description	Kim Handley

Time	Event	Session leader
09:00 – 09:10	Introductions Recap of day 1 Overview of the day	Annie West
09:10 – 10:30	TALK Overview of binning history, key parameters TASK Read mapping TASK Multi-binning strategy with MetaBat and MaxBin	Kim Handley
10:30 – 10:50	Morning tea
10:50 – 11:45	TALK Binning strategies TASK Bin dereplication using DAS_Tool	Kim Handley
11:45 – 12:10	PRESENTATION Alternative approaches to binning	Amali Thrimawithana
12:10 – 13:00	Lunch
13:00 – 15:00	TASK Bin evaluation using CheckM and CheckM2 TALK Bin dereplication across assemblies, working with minimal or non-prokaryotic genomes, and bin refinement strategies TASK Visual bin refinement using VizBin	Kim Handley Mike Hoggard
15:00 – 15:20	Afternoon tea
15:20 – 15:35	TASK Checking VizBin results	Annie West
15:35 – 16:05	TALK Viruses in metagenomic data TASK Identify viral contigs using VirSorter2 and CheckV	Mike Hoggard
16:05 – 16:30	DISCUSSION How will you approach your research question?

Time	Event	Session leader
09:00 – 09:10	Introductions Recap of day 2 Recap of binning outputs Overview of the day	Jian Sheng Boey
09:10 – 10:20	TALK Taxonomic classification: Bin and species determination TASK Taxonomic classification using GTDB-Tk	Annie West
10:20 – 10:40	Morning tea
10:40 – 11:15	TALK Primer to phylogenetic analyses TASK Build a phylogenetic tree using FastTree and visualise tree using iTOL	Jian Sheng Boey
11:15 – 12:05	TASK Exploring results from VirSorter2 and CheckV TALK Predicting viral taxonomy using vConTACT2 TASK (Optional) Visualise vConTACT2 viral gene sharing network in Cytoscape	Mike Hoggard
12:05 – 12:50	Lunch
12:50 – 13:20	TALK Tools for predicting genes: Prodigal, RNAmer, Aragorn, etc. TASK Predict ORFs and protein sequences using Prodigal	Jian Sheng Boey
13:20 – 14:20	TALK Methods for gene annotation TASK Annotate predicted genes using DIAMOND and HMMER3	Jian Sheng Boey
14:20 – 14:50	TALK Using online resources (KEGG, BioCyc, MetaCyc, InterPro, PSORT) TASK View KEGG annotations online TASK View phylogenetic trait distribution using ANNOTREE	Jian Sheng Boey
14:50 – 15:05	Afternoon tea
15:05 – 15:30	PRESENTATION Metagenomic analyses sans binning	Jess Wallbank
15:30 – 15:50	TASK MAG annotation with DRAM TASK Coverage calculation	Annie West
15:50 – 16:00	TASK Group formation and project topic selection	Kim Handley

Time	Event	Session leader
09:00 – 09:10	Introductions Recap of day 3 Overview of the day	Jian Sheng Boey
09:10 – 09:55	TALK Overview of DRAM results TASK Explore DRAM results	Annie West
09:55 – 10:25	TALK Visualising environmental distribution TASK Coverage heatmap and nMDS ordination	Mike Hoggard
10:25 – 10:45	Morning tea
10:45 – 10:55	TASK Workshop survey
10:55 – 12:05	TALK Visualising genomic and metabolic features TASK KEGG metabolic maps TASK Gene synteny	Jian Sheng Boey Annie West
12:05 – 12:55	Lunch
12:45 – 14:40	Group work TASK Analyse data and prepare presentations	Kim Handley Mike Hoggard Annie West Jian Sheng Boey
14:40 – 14:55	PRESENTATION Group presentations	Kim Handley Mike Hoggard Annie West Jian Sheng Boey
14:55 – 15:10	Afternoon tea
15:10 – 15:55	PRESENTATION Group presentations	Kim Handley Mike Hoggard Annie West Jian Sheng Boey
15:55 – 16:00	Wrap up and final discussions	Jian Sheng Boey

Appendices

Appendix ID
Appendix 1	Dereplicating data from multiple assemblies
Appendix 2	Generating input files for "VizBin" from "DAS_Tool" curated bins
Appendix 3	Normalise per-sample coverage values by average library size
Appendix 4	Viral taxonomy prediction via vContact2

Post-workshop survey

Thank you for attending Metagenomics Summer School 2024! We would like your feedback on how we have done and what we can improve on. You can provide feedback here.

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: