Welcome to Metagenomics Workshop!

Welcome to the one-day metagenomics assembly workshop. This tutorial will guide you through the typical steps of metagenome assembly and binning.

• Setting up your de.NBI Cloud SimpleVM instance
• Command Line Introduction: Excercises
  • Excercise 1: Basic File Operations
  • Excercise 2: Links
  • Excercise 3: Display File Content
  • Excercise 4: Wildcards
  • Excercise 5: grep and wc
  • Excercise 6: Streams
  • Excercise 7: Tabular Data
• The Tutorial Data Set
• FastQC Quality Control
  • Quality Treatment
  • Run fastp on a PE library
  • Run FastP again
  • Trimming adapter sequence
• Assembly
  • Velvet Assembly
  • MEGAHIT Assembly
  • metaSPAdes Assembly
  • IDBA-UD Assembly
  • Ray Assembly
• Assembly Evaluation
  • Read Mapping
  • MetaQUAST
• Binning
  • MaxBin Binning
  • MetaBAT Binning
  • Assessing bin quality
• Classification
  • Genome Taxonomy Database (GTDB)
• Data submission to ENA
  • Data submission to ENA - Intro
  • Submitting a study
  • Submitting an environment sample
  • Submitting reads
  • Submitting a metagenome assembly
  • Submitting a bin sample
  • Submitting a metagenome bin
  • Annotating a MAG and prepare it for ENA submission
  • Submitting a MAG sample
  • Submitting a MAG
• Nextflow / nf-core
  • Nextflow
  • nf-core assembly and binning
  • nf-core pipeline for taxonomy profiling
  • nf-core hands-on