Training materials
Target audience: Students
and Authors: Alex Ostrovsky or Bazante Sanders or Bori Mifsud or Kathi Zarnack or Maria Lehtivaara or The Carpentries or allegra.via Via
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hands-on tutorial
Data visualisation Olympics - Visualization in R
• beginnerSoftware engineering Foundations of Data Science R cyoa jupyter-notebook rmarkdown-notebook -
hands-on tutorial
Identification of AMR genes in an assembled bacterial genome
• beginnerWhole genome sequencing Public health and epidemiology Genomics Microbiology Sequence analysis Infectious disease Antimicrobial Resistance Genome Annotation amr gmod illumina jbrowse1 microgalaxy one-health -
hands-on tutorial
Python - Coding Style
•• intermediateSoftware engineering Foundations of Data Science jupyter-notebook -
hands-on tutorial
Virtual Environments For Software Development
•• intermediateSoftware engineering Foundations of Data Science jupyter-notebook -
hands-on tutorial
Conda Environments For Software Development
•• intermediateSoftware engineering Foundations of Data Science conda jupyter-notebook -
hands-on tutorial
Python - Testing
•• intermediateSoftware engineering Foundations of Data Science jupyter-notebook -
hands-on tutorial
Calling variants in non-diploid systems
• beginnerGenetic variation Genomics Sequence assembly DNA polymorphism Microbiology Sequence analysis Variant Analysis microgalaxy prokaryote -
hands-on tutorial
Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)
• beginnerSequence assembly Whole genome sequencing Public health and epidemiology Genomics Microbiology Antimicrobial Resistance Assembly amr assembly gmod jbrowse1 microgalaxy nanopore -
hands-on tutorial
VGP assembly pipeline: Step by Step
•• intermediateSequence assembly Assembly VGP eukaryote pacbio -
hands-on tutorial
VGP assembly pipeline - short version
•• intermediateSequence assembly Assembly VGP eukaryote pacbio