Welcome!
Summer Nanopore Sequencing and Bioinformatics Workshop
Syllabus / Documents
(all times are Mountain Daylight Time. File links are updated frequently, please refresh your browser for latest files)
(all times are Mountain Daylight Time. File links are updated frequently, please refresh your browser for latest files)
Week 1 |
Monday - |
Tuesday - |
Wednesday - |
Thursday - |
Friday - |
AM Session: 9-12 |
Workshop Logistics: Ethan Workshop, NMINBRE and NCGR Introduction: Callum Red Alder / Nodule Introduction: Callum Student/instructor Introductions |
What is DNA Extraction? (Adam) How does a Minion work? Overviews of analysis: Adam |
Outline to sample/seq workflow: Callum Metagenome Bioinformatics Nodule Processing Lecture: Callum |
What are: Library Prep / synthesis, gDNA amplifiation, End prep: Adam Begin Lib prep for use in MinIon: Adam |
How to use MinIon, Complete lib prep: Adam |
Lunch 12-1 |
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PM Session: 1-5 |
Continuation of Alder/Nodule Field Trip to Collect Samples |
Lab Equip tour/tutorial Lab practice: Dilution and concentration exercise / Strawberry exercise? |
Nodule Sterilization / Pulverization: Callum E.Z.N.A. Bacterial DNA Extraction Kit Lecture: Adam DNA Quantification: Adam |
Write up methods: Student time |
Load samples and begin MinIon Seq (1st 4 samples). Runs are 72 hours What is Seq Analysis?: Adam Continue methods |
Exercises |
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Week 2 |
Monday 7/4 |
Tuesday 7/5 |
Wednesday 7/6 |
Thursday 7/7 |
Friday 7/8 |
AM Session: 9-12 |
OFF FOR HOLIDAY |
Check MinIons. Talk about results so far. Chance to re-load/restard if needed (before weekend) |
Systems Intro Installs Linux Intro: Ethan |
Read Classification Kraken/2/uniq: Callum |
Contig/Metagenome Assembly - Fly/Metafly/Canu: Evan |
Lunch 12-1 |
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PM Session: 1-5 |
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Analysis workflow breakdown What is Quality Control? What are contigs/binning?: Adam |
Pyco QC: Adam Removal of Alder Seq Reads - Samtools, MiniMap2: Joann |
assembly section (Canu): Evan |
Binning - VAMB: Callum |
Exercises |
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Week 3 |
Monday 7/11 |
Tuesday 7/12 |
Wednesday 7/13 |
Thursday 7/14 |
Friday 7/15 |
AM Session: 9-12 |
Bin Classification - CAT/BAT: Callum |
Annotation - Prokka: Joann |
How to we visualize output/results? Visualization - Pavian; Evan |
Writing up results |
Results Presentations/Colloquium |
Lunch 12-1 |
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PM Session: 1-4 |
Gene Search - BLAST Nitrogen Fixation Gene Search (Nitrogenase genes) Nodulation Gene Search: Adam |
Visualization cont: Joann |
Group share |
Closing, Feedback Survey |
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Exercises |
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