Metagenomics Summer School

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.

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Useful locations and links

Working directories

For all exercises after the bash introduction, you will be working from the file path

/nesi/nobackup/nesi02659/MGSS_U/YOUR_USERNAME/

bash/slurm cheatsheet

A few helpful commands and shortcuts for working in bash or with slurm can be found here.

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:

• FastQC results
• Quast results
• Input files for VizBin
• Tables of gene annotations
• DRAM output files

Slides for workshop

You can find a copy of the slides presented during the workshop, with published figures removed, in the slides/ folder.

Etherpad

We will be using a collaborative document to share long code, results, or even code errors. This document can be found here or type https://etherpad.wikimedia.org/p/MGSS_17_11_20 in your browser.

Post-Workshop Survey

Please complete the survey before you leave to help us continue to provide A+ workshops

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Workshop exercises

Day 1

1. Bash scripting
2. Quality filtering raw reads
3. Assembly (part 1)
4. Assembly (part 2)
5. Evaluating the assembly

Day 2

1. Binning (part 1, read mapping)
2. Binning (part 2, initial binning)
3. Binning (part 3, dereplication)
4. Bin refinement

Day 3

1. Viruses
2. Coverage and Taxonomy
3. Gene prediction
4. Gene annotation (part 1)
5. Gene annotation (part 2)

Day 4

1. Gene annotation (part 3)
2. Presentation of data

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Timetable

Day 1 - 17^th November 2020

Time	Event	Session leader
9:00 am – 9:30 am	Introduction - Welcome - Logging into NeSI	Michael Hoggard
9:30 am – 10:30 am	TASK: Bash scripting	Ngoni Faya
10:30 am – 10:50 am	Morning tea break
10:50 am – 11:30 am	TASK: Bash scripting (continued)	Ngoni Faya
11:30 am – 12:00 pm	TALK: The metagenomics decision tree	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 TASK: Common issues and best practice	Carmen Astudillo-Garcia
1:45 pm – 3:00 pm	TASK: Run IDBA_UD assembly TALK: Assembly - Choice of assemblers - Considerations for parameters, and when to stop! TASK: Exploring assembler options TASK: Submitting jobs to NeSI via slurm TASK: Run SPAdes 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	Michael Hoggard

Day 2 - 18^th November 2020

Time	Event	Session leader
9:00 am – 9:15 am	Introduction - Overview of yesterday, questions - Overview of today	Carmen Astudillo-Garcia
9:15 am – 9:30 am	TALK: Automation, reproducibility, and FAIR principles	Dan Jones
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	TALK: Overview of binning history (continued) - Key parameters and strategies for binning	Kim Handley
11:20 am – 12:00 pm	Binning (part 2) TASK: Multi-binning strategy (Metabat and Maxbin)	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	Michael Hoggard
2:00 pm - 3:00 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 TALK: Bin refinement - Refinement strategies -	Carmen Astudillo-Garcia Michael Hoggard
3:00 pm – 3:20 pm	Afternoon tea break (Tea, coffee, and snacks provided)
3:20 pm – 5:00 pm	TALK: Bin refinement - Refinement strategies (cont) - VizBin and ESOMana TASK: Working with VizBin TASK: Submit VIBRANT job	Michael Hoggard

Day 3 - 19^th November 2020

Time	Event	Session leader
9:00 am – 9:30 am	Introduction - Overview of yesterday, questions - Overview of today	Michael Hoggard
9:30 am – 10:30 am	TASK: Identifying viral contigs (VIBRANT) TALK: Identifying viruses from metagenomic data TASK: QC of viral contigs (CheckV) TASK: Coverage calculation (bowtie) TASK: Taxonomic classification (Bin taxonomy with GTDB-TK; viral taxonomy predictions with vConTACT2)	Michael Hoggard David Waite
10:30 am – 10:50 am	Morning tea break (Tea, coffee, and snacks provided)
10:50 am – 11:30 am	TALK: Gene prediction, using prodigal, and other tools (RNAmer, Aragorn, etc) TASK: Predict open reading frames and protein sequences	David Waite
11:30 am – 12:00 pm	TALK: Gene annotation (part 1) TASK: Gene annotation using diamond and hmmer Discussion: Evaluating the quality of gene assignment Discussion: Differences in taxonomies (GTDB, NCBI etc)	Carmen Astudillo-Garcia
12:00 pm – 12:45 pm	Break for lunch (lunch not provided)
12:45 pm – 2:00 pm	TALK: Gene annotation (part 2) - Using online resources (e.g. KEGG, BioCyc, MetaCyc, HydDB, PSORT) TASK: View KEGG annotation in KEGG website	Christia Straub Florian Pichlmueller
2:00 pm – 3:00 pm	TALK: Bin taxonomic classification - Bin and species determination TASK: View phylogenetic trait distribution (ANNOTREE)	David Waite
3:00 pm – 3:20 pm	Afternoon tea break
3:20 pm – 4:30 pm	TASK: MAG annotation with DRAM TASK: Introduce group project goals TASK: Dividing into working groups / get a group name TASK: Select a goal from your project	Carmen Astudillo-Garcia
4:30 pm – 5:00 pm	End of day wrap up	Kim Handley

Day 4 - 20^th November 2020

Time	Event	Session leader
9:00 am – 9:15 am	Introduction - Overview of yesterday, questions - Overview of today	Michael Hoggard
9:15 am – 10:00 am	TALK: DRAM results overview TASK: Explore DRAM results	Carmen Astudillo-Garcia
10:00 am – 10:30 am	Presentation of data TALK: Visualising findings (metabolism maps, heatmaps, cell schematics, gene trees, gene maps) TASK: Coverage heatmap / Ordination (Optional)	Michael Hoggard
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 (continued) TALK: Visualising findings (metabolism maps, heatmaps, cell schematics, gene trees, gene maps) TASK: KEGG metabolic pathways TASK: Gene synteny TASK: CAZy heatmaps (Optional)	Carmen Astudillo-Garcia Boey Jian Sheng Hwee Sze Tee
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	Carmen Astudillo-Garcia
3:40 pm – 4:00 pm	End of day wrap up - Final discussion	Kim Handley Michael Hoggard

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