biom-format

What it is and what it does

biom-format is a Python library for working with the BIOM (Biological Observation Matrix) file format, a standard in microbiome and metagenomic research for storing abundance data—counts of observations such as OTUs, KO categories, or lipid types across multiple biological samples. It provides read/write access to BIOM files, typically in HDF5 format, and allows you to load, manipulate, and export these matrices for downstream analysis.

The package depends on numpy, scipy, pandas, h5py, and click, making it suitable for integration into data pipelines. It supports Python 3.9 through 3.13 on major platforms. The library is designed to be a general-purpose container for observation counts from various high-throughput biological assays.

Use it for:

• Load and parse BIOM files from microbiome pipelines for downstream statistical analysis.
• Convert between BIOM and tabular formats for integration with other analysis tools.
• Manipulate sample metadata and observation taxonomy within a BIOM matrix programmatically.
• Export abundance tables from your own analysis pipeline in the standard BIOM format.
• Batch process multiple BIOM files to extract subsets of samples or observations.

Worth the install?

AI-flagged interpretation of the facts on this page — verify before relying

Reads, writes, and manipulates Biological Observation Matrix (BIOM) files, a standard format for storing counts of observations across biological samples.

Yes, if you work with microbiome or metagenomic data in BIOM format. The package is stable, permissively licensed, and widely compatible across platforms and Python versions. However, maintenance is aging (last release 353 days ago), so verify that it meets your specific pipeline requirements before committing to it for production workflows. No known security vulnerabilities.

Install

biom-format on PyPI

pip install biom-format

uv add biom-format

poetry add biom-format

Installing biom-format

Before you install

Medium install friction due to compiled dependencies (numpy, scipy, h5py). Wheels available for Python 3.9–3.13 on macOS, Linux, and Windows. Last release 353 days ago; maintenance status is aging, so expect slower response to issues.

License in practice

BSD license is permissive; you may use, modify, and distribute this package freely in commercial and private projects with minimal restrictions.

Quickstart

pip install biom-format

import biom
table = biom.load_table('data.biom')
print(table.shape)

Requires h5py, which depends on HDF5 system libraries; installation may require a C compiler or prebuilt wheels for your platform.

Verify before relying

• Whether the package actively maintains compatibility with major microbiome analysis pipelines.
• Performance characteristics for large matrices.
• Availability of comprehensive documentation beyond the homepage.

Package facts

Evidence: biom_format-2.1.17-cp310-cp310-macosx_10_9_x86_64.whl; biom_format-2.1.17-cp310-cp310-macosx_11_0_arm64.whl; biom_format-2.1.17-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl; biom_format-2.1.17-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl; biom_format-2.1.17-cp310-cp310-win_amd64.whl; biom_format-2.1.17-cp311-cp311-macosx_10_9_x86_64.whl; biom_format-2.1.17-cp311-cp311-macosx_11_0_arm64.whl; biom_format-2.1.17-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl; biom_format-2.1.17-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl; biom_format-2.1.17-cp311-cp311-win_amd64.whl; biom_format-2.1.17-cp312-cp312-macosx_10_13_x86_64.whl; biom_format-2.1.17-cp312-cp312-macosx_11_0_arm64.whl; biom_format-2.1.17-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl; biom_format-2.1.17-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl; biom_format-2.1.17-cp312-cp312-win_amd64.whl; biom_format-2.1.17-cp313-cp313-macosx_10_13_x86_64.whl; biom_format-2.1.17-cp313-cp313-macosx_11_0_arm64.whl; biom_format-2.1.17-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl; biom_format-2.1.17-cp313-cp313-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl; biom_format-2.1.17-cp313-cp313-win_amd64.whl

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