This tool can open metagenome files, filter them by taxonomy, and output filtered results for further analysis. The tool can also do some basical statistcial analysis, like summing the function abundance per sample location, and function abundance per sample location + taxonomy.
If you are building from source, run dotnet run to build, restore and run the tool. The tool provides you with two actions:
- process - parses the metagenome input files (contribution and description), filters them by taxonomy, and outputs filtered result
- generate - uses the filtered result to run a simple statistical analysis and outputs visualisation-friendly results
All result files are valid TSV files.
Running from Windows
mia-viz.exe process -c "/path/to/contribution.tsv.gz" -t "/path/to/taxonomy.tsv"
Running from source
dotnet run process -- -c "/path/to/contribution.tsv.gz" -t "/path/to/taxonomy.tsv"
Parameters:
- -c -> path to contribution tsv.gz file
- -t -> path to taxonomy tsv file
Running from Windows
mia-viz.exe generate -t Microbacil Macrobacil
Running from source
dotnet run generate -- -t Microbacil Macrobacil
Parameters:
- -t -> list of taxons to include in the generate statistical analysis files
All output files can be found in the tool's ./output subdirectory.
Run the following command to build a self contained, Win 64 or OSX ARM 64 compatible executable You can find the Release ID nomenclature here: https://learn.microsoft.com/en-us/dotnet/core/rid-catalog
dotnet publish -c Release -r win-x64 --self-contained true
dotnet publish -c Release -r osx.13-arm64 --self-contained true