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:
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 currently offers three commands corresponding to the main use-cases. You can find out more in the commands documentation.
Copyright¶
- Copyright © 2022, Moritz E. Beber, Maxime Borry, James A. Fellows Yates, and Sofia Stamouli.
- Free software distributed under the Apache Software License 2.0.