Welcome to Capalyzer!

Capalyzer is a python package to summarize and parse metagenomic data. Capalyzer takes output from the MetaSUB Core Analysis Pipeline and builds summary data tables. After the data tables have been built capalyzer includes utilities to parse those tables.

Capalyzer aims to remove boilerplate code from metagenomic analyses and provide a consistent interface for secondary analyses. Capalyzer is a comkunity project and is easy to contribute to.

Capalyzer in three points:

  • Tidy and rich summaries of metagenomic analyses
  • Consistent and clean API for parsing files
  • Common statistical and ecological analyses built in

What does it look like?

from capalyzer.packet_parser import DataTableFactory

table_factory = DataTableFactory(<data packet dir>)

taxa_richness = table_factory.taxa_alpha_diversity(metric='richness')
taxa_tbl = table_factory.taxonomy()
amr_tbl = table_factory.amrs()
hmp_tbl = table_factory.hmp()

You can get the library directly from PyPI:

pip install capalyzer

Documentation

This part of the documentation guides you through all of the library’s usage patterns.

Miscellaneous Pages