AxioParse: Processed Axiom Microbiome Array Data

AxioParse is a Python pipeline that automates the processing of outputs from the Applied Biosystems Axiom Microbiome Array, which detects bacteria, archaea, viruses, protozoa, and fungi. The pipeline consolidates probe-level data into species-level tables, updates taxonomy using NCBI Entrez, and exports formatted datasets for downstream analysis in tools like QIIME2 and R. It addresses a lack of open-source tools for handling this specific microarray's native outputs.

Use Cases

• Automating data cleaning and taxonomic mapping of Axiom Microbiome Array outputs based on the described pipeline functionality.
• Generating species-level abundance tables from probe-level MiDAS data for community analysis.
• Preparing formatted datasets compatible with downstream analysis platforms like QIIME2 and R.
• Improving reproducibility in microbiome studies by standardizing the preprocessing of Axiom array data.

Strengths

• The associated pipeline, AxioParse, is open-source and built on the Dagster orchestration framework for automation.
• The dataset or pipeline output is licensed under CC-BY-4.0, facilitating reuse.
• The pipeline specifically addresses a gap in tools for the Axiom Microbiome Array, targeting a high-throughput assay for diverse microbial taxa.

Limitations

• The dataset's exact structure, row count, and column details are not specified in the provided metadata.
• The 'last updated' date of 2026-03-18 is a future date, which creates a conflict and casts doubt on the temporal accuracy of the metadata.
• The provenance and specific content of the example datasets referenced in the description are unclear.

Provenance

Source

Pranav Kirti, associated with the Eghtesady Lab Bioinformatics GitHub repository.

Collection Method

Likely generated by the AxioParse pipeline from raw Axiom Microbiome Array outputs.

Freshness

2026-03-18 09:54:17