Training materials
Authors: Bazante Sanders or Delphine Lariviere
and Contributors: Allegra Via or Anton Nekrutenko or David Philip Judge or Elisabeth Busch or Helena Rasche or JuliaAcademy
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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
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
Making sense of a newly assembled genome
• beginnerSequence assembly Genomics Microbiology Assembly gmod jbrowse1 microgalaxy prokaryote -
hands-on tutorial
Unicycler Assembly
• beginnerSequence assembly Genomics Microbiology Assembly microgalaxy prokaryote -
hands-on tutorial
Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data
• beginnerSequence assembly Whole genome sequencing Public health and epidemiology Genomics Microbiology Assembly assembly illumina microgalaxy -
hands-on tutorial
Python - Subprocess
•• intermediateSoftware engineering Foundations of Data Science jupyter-notebook -
hands-on tutorial
Python - Globbing
•• intermediateSoftware engineering Foundations of Data Science jupyter-notebook -
hands-on tutorial
Make & Snakemake
•• intermediateSoftware engineering Foundations of Data Science -
hands-on tutorial
Python - Try & Except
• beginnerSoftware engineering Foundations of Data Science jupyter-notebook -
hands-on tutorial
Python - Files & CSV
• beginnerSoftware engineering Foundations of Data Science jupyter-notebook