TAXPASTA Documentation¶

TAXonomic Profile Aggregation and STAndardisation

About¶

The main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler. In future, we also intend to offer methods for forming a consensus for the same sample analyzed by different profilers.

Supported Taxonomic Profilers¶

Taxpasta currently supports standardisation and generation of comparable taxonomic tables for:

Bracken
Centrifuge
DIAMOND
Kaiju
Kraken2
KrakenUniq
MEGAN6/MALT via rma2info which converts their RMA6 output files into a tabular format
MetaPhlAn
mOTUs

See supported profilers for more information.

Install¶

It's as simple as:

pip install taxpasta

Usage¶

The main entry point for taxpasta is its command-line interface (CLI). You can interactively explore the offered commands through the help system.

taxpasta -h

Taxpasta currently offers three commands corresponding to the main use-cases. You can find out more in the commands documentation.

Copyright¶

Free software distributed under the Apache Software License 2.0.