Welcome to…

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…a Snakemake workflow streamlining taxonomic and functional annotation of metagenomes and metagenome-assembled genomes (MAGs). It takes raw sequencing reads, assembles and annotates contigs, and outputs colorful graphics and rich tables. You can choose between different types of input read formats (paired-end or interleaved), annotation databases (eg. PFAM, KEGG, CAZy), and more.

If in doubt, reach out!

If you have any questions or issues to report, please go to GitHub and open a New issue.

Content

• Getting started
  • Install Mamba
  • Get annoSnake
  • Running with example data, download from Figshare
  • Running annoSnake locally
  • Running annoSnake with other scheduling systems
• The annoSnake workflow: step by step
  • Input data
  • ./profile/params.yaml file
  • ./profile/config.yaml file
  • Metagenome assembly
  • Taxonomic annotation
  • Functional annotation
  • Abundance calculation of gene families
  • Metagenome-assembled genomes (MAGs)
  • Fresh Install
• Databases
  • Install Databases
  • In general
• Output
  • Tables
  • Figures
• Workflow overview