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Disclaimer (delete this in your fork)

This is the main repository! If you are planning a new workshop, fork this one and adjust everything you need in your forked repository. If you want to add new content or update existing tools/commands, consider to do these changes first into this main repository via a Pull Request and before you start working on your own workshop specifics!

Below, you find all content of this repository. Please also notice the placeholders "<...>" theat you should adjust!


Workshop Nanopore Bioinformatics

A practical introduction to <...> for <...> in the context of the <...> project.

Schedule links for the workshop

General

Long-read bacteria genome reconstruction

SARS-CoV-2 data science

Long-read metagenomics

Instructors

  • <...>, <...>, and <...>

Schedule

All events are held at <...>, room <...>

SOMEDAY, DATE

Time Welcome, Linux re-cap, container & WMS
10:00-10:30 Welcome & introduction
10:30-12:00 Linux re-cap
12:00-13:00 Lunch break
13:00-14:00 Container & WMS
14:00-14:30 Coffee break
14:30-16:00 Hands-on & demo
16:00-16:15 Wrap-up & questions

SOMEDAY, DATE

Time Nanopore
09:00-10:00 Debriefing previous day
10:00-11:00 Nanopore intro
12:00-13:00 Lunch break
13:00-13:30 Nanopore basecalling & data fromats
13:30-14:00 Nanopore QC
14:00-14:30 Coffee break
14:30-16:00 Hands-on & demo (ONT isolate)
14:30-16:00 Hands-on & demo (metagenomics)
16:00-16:15 Wrap-up & questions

SOMEDAY, DATE

Time De novo assembly and mapping
09:00-10:00 Debriefing previous day
10:00-10:45 De novo Assembly
10:45-11:00 Coffee break
11:00-12:00 Mapping & Visualization
12:00-13:00 Lunch break
13:00-14:30 Hands-on & demo
14:30-15:00 Coffee break
15:00-15:45 Continue practical session
15:45-16:00 Wrap-up & questions

SOMEDAY, DATE

Time Assembly polishing and variant calling
09:00-10:00 Debriefing previous day
10:00-10:45 Assembly polishing
10:45-11:15 Coffee break
11:15-12:00 Variant calling
12:00-13:00 Lunch break
13:00-14:30 Hands-on & demo
14:30-15:00 Coffee break
15:00-15:45 Continue practical session
15:45-16:00 Wrap-up & questions

SOMEDAY, DATE

Time The Rest & Open Questions
09:00-10:00 Debriefing previous day
10:00-11:00 Miscellaneous (bacteria)
11:00-12:00 Hands-on & demo
12:00-12:30 Wrap-up & questions

SOMEDAY, DATE

Time SARS-CoV-2 Introduction
09:00-10:00 Debriefing previous day
10:00-11:00 FU course intro
11:00-12:00 RKI Genomic Surveillance and SARS-CoV-2

SOMEDAY, DATE

Time SARS-CoV-2 sequencing & genome reconstruction
09:00-10:00 Debriefing previous day
10:00-11:00 Sequencing (SARS-CoV-2)
11:00-12:00 SARS-CoV-2 genome reconstruction
12:00-13:00 Lunch break
13:00-14:30 Hands-on & demo
14:30-15:00 Coffee break
15:00-15:45 Continue practical session
15:45-16:00 Wrap-up & questions

SOMEDAY, DATE

Time SARS-CoV-2 evolution, mutation profiling & phenotypization
09:00-10:00 Debriefing previous day
10:00-11:00 SARS-CoV-2 genome organisation & evolution
10:00-11:00 SARS-CoV-2 epistasis and variants
12:00-13:00 Lunch break
10:00-11:00 SARS-CoV-2 nomenclature
11:00-12:00 SARS-CoV-2 mutation profiling
14:30-15:00 Coffee break
13:00-14:30 Hands-on & demo
15:00-15:45 Continue practical session
15:45-16:00 Wrap-up & questions

SOMEDAY, DATE

Time SARS-CoV-2 pathogen evolution & incidence estimation
09:00-10:00 Debriefing previous day
10:00-12:00 SARS-CoV-2 pathogen evolution and genome-based incidence estimation
12:00-13:00 Lunch break
13:00-14:00 SARS-CoV-2 risk score via VOCAL
14:30-15:00 Coffee break
13:00-14:30 Hands-on & demo
15:00-15:45 Continue practical session
15:45-16:00 Wrap-up & questions

SOMEDAY, DATE

Time SARS-CoV-2 phylogeny & outbreak investigation
09:00-10:00 Debriefing previous day
10:00-12:00 Phylogeny and outbreak investigation
12:00-13:00 Lunch break
13:00-14:00 Outbreak detection & clustering via breakfast
14:30-15:00 Coffee break
13:00-14:30 Hands-on & demo
15:00-15:45 Continue practical session
15:45-16:00 Wrap-up & questions

SOMEDAY, DATE

Time Metagenomic read classification
09:00-10:00 Debriefing previous day
10:00-12:00 Metagenomic read classification
12:00-13:00 Lunch break
13:00-14:30 Hands-on & demo
14:30-15:00 Coffee break
15:00-15:45 Continue practical session
15:45-16:00 Wrap-up & questions

SOMEDAY, DATE

Time Metagenome assembly, binning, and annotation
09:00-10:00 Debriefing previous day
10:00-11:00 Metagenome-assembled genomes (MAGs)
11:00-12:00 MAG quality and gene annotation
12:00-13:00 Lunch break
13:00-14:30 Hands-on & demo
14:30-15:00 Coffee break
15:00-15:45 Continue practical session
15:45-16:00 Wrap-up & questions

Acknowledgement

This course material is partly based on the following resources and on contributions from great people (no specific order):

  • Martin Hoelzer, RKI MF1, content about Linux, container, Nextflow, sequencing, genomic surveillance & glueing everything together
  • Sebastian "Raverjay" Krautwurst, FSU Jena, some Linux and ONT content
  • Stephan Fuchs, RKI MF1, some Linux and Assembly content, Slides on SARS-CoV-2 nomenclature & phylogeny
  • Matt Huska, RKI MF1, automatic test script for all md code blocks using codedown and general help
  • Workshop structure inspired by https://github.com/cinemaparis/2023
  • Some ONT intro slides from Josh Quick, original
  • Nanopore long-read bioinformatics tutorial from timkahlke
  • Max von Kleist, RKI P5 and FU Berlin, basically most content about sequencing and SC2 data science (evolution, epistasis, incidence esitmation, ...)
  • Maureen Smith, Maria Trofimova, RKI P5 and FU Berlin, content on Incidence estimation
  • Hugues Richard, RKI MF1, content about SC2 risk assessment
  • Matt Huska & Denis Beslic, RKI MF1, content about SC2 outbreak detection & clustering

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Main resource for practical introductions to long-read bioinformatics.

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