PoreCamp Australia 2017
A bootcamp to learn about operating the Oxford Nanopore MinION
Itinerary for PoreCampAU
Day 1: Library Preparation and running the MinION.
- 10am Start: Meet/Greet Introduction : Location
- How does nanopore sequencing work? - 1D reads vs 2D reads.
- How to purify High-Molecular Weight DNA samples.
- Prepare samples for nanopore sequencing:
- Using MinKNOW.
- Platform QC of flowcells.
- Preparing the library for the MinION run.
- Loading the library onto the flowcell.
- Monitoring and assessing your run.
Day 2: Bioinformatics
- Handling MinION data file types (WTF: What the Fast5?)
- Compare raw MinION output to Metrichor output.
- Overview of raw attributes.
- How to diagnose what went wrong in the lab with bioinformatics.
- Sorting fast5 files by their metrichor workflow.
- Metagenomics - WIMP (What's in my pot?).
- Alignment, best tools to align your MinION data.
- Visualising your alignment consensus.
- Error correcting MinION reads.
- De novo assembly - best tools for de novo assembly of long read data.
- Scaffolding reads using the MinION, visualise the output.
- Best tools for hybrid assembly.
- Best tools for long-read analysis.
- Local basecalling. What options are out there?
- Compare the alignments of local basecalling to that of Metrichor.
Day 3: Putting it all together
- Aligning your sequencing runs.
- Understanding the Metrichor output of your runs.
- Comparison of Day 1 sequencing runs.
- Reflections of nanopore sequencing.
- Finish 4pm.