Taxconverter

A lightweight tool for one purpose only: to unify the outputs of different taxonomic classifiers. Currently supports Centrifuge v1.0.4, Kraken2 v2.1.3, Metabuli v1.0.1 and MetaMaps v.633d2e. The output files of these tools are converted to MMseqs2 format.

Having everything converted to MMseqs2 format means the output file will only have two informative columns: sequence identifiers (the 1st column) and taxonomic labels on all levels from domain to species concatenated with ";" (9th column). The rest is filled with zeros or by trivial parsing.

Suggestions and contributions are most welcome.

Installation

1. Clone this repo and install the package from the source (releasing pip package WIP).

git clone git@github.com:RasmussenLab/taxconverter.git
cd taxconverter
pip install -e .

2. Unzip the two files from data/lineage.zip (38.3 MB): ncbi_lineage.csv (246.2 MB) and metabuli_lineage.csv (58.1 MB), and place them to the data/ folder.

Usage

To convert Centrifuge, Kraken2 and MetaMaps outputs, provide one file with the taxonomy annotation results:

taxconverter centrifuge -i centrifuge_annotations.tsv -o result.tsv

taxconverter kraken2 -i kraken2_annotations.tsv -o result.tsv

taxconverter metamaps -i metamaps_annotations.tsv -o result.tsv

To convert a Metabuli output, provide two files with _classifications.tsv and _report.tsv postfixes:

taxconverter metabuli -c metabuli_classifications.tsv -r metabuli_report.tsv -o result.tsv

For more help, run taxconverter -h, taxconverter metabuli -h, taxconverter centrifuge -h, taxconverter kraken2 -h, taxconverter metamaps -h

References and links

This package is made to complement the Taxometer tool for refining taxonomic annotations from any classifier using contigs k-mers and co-abundances (preprint).

Other links:

• MMseqs2 Article Github
• Metabuli Article Github
• Centrifuge Article Github
• Kraken2 Article Github
• MetaMaps Article Github