Welcome! This repository contains a variety of scripts that are useful for metagenomics work. Detailed usage instructions can be found within the folders.
Contains a Jupyter notebook (Compare-kreport-taxonomic-profiles.html) demonstrating how to compare kraken reports across multiple samples for specified taxonomic ranks, including how to:
- Generate and save a combined taxon count table for a particular taxonomic rank
- Create and save stacked barplots showing relative or absolute abundances of taxa across samples
- Perform analyses at different taxonomic ranks (strains, species, genera, families, etc.)
Contains several scripts for converting the output file formats for taxonomic profilers to kraken and metaphlan report formats:
Convert_kreport_to_mpa.py: Convert any kraken report (kreport) file into metaphlan (mpa) format.Convert_MEGAN-RMA-NCBI-c2c_to_kreport-mpa.py: Convert taxonomic counts from MEGAN6 into kraken report (kreport) and metaphlan (mpa) formats.Convert_metamaps-WIMP_to_kreport-mpa: Convert the output of Metamaps into kraken report (kreport) and metaphlan (mpa) formats.Convert_metaphlan3_mpa_to_kreport: Convert the output of MetaPhlAn3 into kraken report (kreport) format.
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