Benchmarking Strain-Level Profiling of E. Coli in Gut Metagenomes

Supplementary data files from a 2026 benchmarking study on strain-level profiling of Escherichia coli in short-read gut metagenomes. The repository includes normalized relative abundances for 98 species assemblies, raw predicted abundance data for ZymoBIOMICS and mock community datasets, and simulated metagenomes data with detection metrics. It was authored by Matthew Galbraith and is licensed under CC-BY-4.0.

Use Cases

• Benchmarking strain-level profiling tools based on simulated metagenomes with known references.
• Evaluating the impact of human read depletion on microbial abundance predictions using the SRR13355226 mock community data.
• Comparing predicted relative abundances from different reference databases using the simulated datasets with reduced references.
• Analyzing detection sensitivity and call type assignments across increasing detection thresholds in simulated data.

Strengths

• Includes data from a controlled ZymoBIOMICS gut microbiome standard, providing a known benchmark.
• Contains simulated metagenomes with detection metrics across thresholds, useful for sensitivity analysis.
• Provides raw data for 98 species assemblies used to construct a baseline gut microbiome profile.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Data may reflect bias inherent to the specific simulation and benchmarking methodology described.

Provenance

Source

Supplementary data from the study 'Benchmarking strain-level profiling of Escherichia coli in short-read gut metagenomes' (Galbraith et al., 2026).

Collection Method

Likely generated from metagenomic sequencing simulations, mock community analyses, and computational profiling tools.

Freshness

Last updated 2026-05-15 08:51:10