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

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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:

Github Binder:

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