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. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts.

Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table. 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:

See supported profilers for more information.

Install¶

It's as simple as:

pip install taxpasta

Taxpasta is also available from the Bioconda channel

conda install -c bioconda taxpasta

and thus automatically generated Docker and Singularity BioContainers images also exist.

Optional Dependencies¶

Taxpasta supports a number of extras that you can install for additional features; primarily support for additional output file formats. You can install them by specifying a comma separated list within square brackets, for example,

pip install 'taxpasta[rich,biom]'

rich provides rich-formatted command line output and logging.
arrow supports writing output tables in Apache Arrow format.
parquet supports writing output tables in Apache Parquet format.
biom supports writing output tables in BIOM format.
ods supports writing output tables in ODS format.
xlsx supports writing output tables in Microsoft Excel format.
all includes all of the above.
dev provides all tools needed for contributing to 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.