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MAGstats - Visualizing the completeness and redundancy of MAGs and draft genomes

Quick Start

  • Launch the binder with the button above. This will take a few minutes to load.
  • Upload your newick tree and metadata file to the example_data folder via the upload button.
  • Launch the R Jupyter notebook by clicking index.ipynb
  • Change the necessary file names 
    nwk_file <- "GToTree_output.newick"
bin_metadata_file <- "MED_metadata.tsv"
  • Execute the code blocks to generate the final figure

Example Output

  • Example Output

Summary

  • Designed to visualize various quality metrics for MAGs and draft genomes
  • The immediate input for MAGstats are a newick tree file and a metadatafile
    • A newick tree file can be generated using GToTree
    • A metadata file can be generated using the qa option in CheckM
      • MAGstats only requires five columns from the CheckM output with the names MAG_ID Length Completion Redundancy GC_Content
      • Column names must exactly match these five in a tab-delimited format
      • Necessary columns can be selected in Excel and exported as a TSV
  • The output displays the phylogenetic tree of MAGs and genomes with corresponding quality information. MAGstats can be used to explore the quality of a set of MAGs and/or genomes for downstream analysis

Authors

  • Shengwei Hou, housw, 0000-0002-4474-7443

Links

Zenodo Binder, doi: DOI

Github Binder: Binder

Github Repository: https://github.com/speeding-up-science-workshops/MAGstats-binder/