ArticleBioinformatics advances2026
FetchM: streamlining genome and metadata integration for bacterial comparative genomics.
Article in Bioinformatics advances, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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3 authors.
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Abstract
Motivation: Large-scale bacterial comparative genomics require comprehensive metadata describing genome assemblies and their biological context. While NCBI Genome holds the assemblies and BioSample stores key contextual fields such as collection date, host, and location, the lack of integration requires researchers to manually merge the two sources, slowing large-scale comparative studies. To address the gap, we built FetchM, a Python-based tool for automated retrieval, integration, analysis, and visualization of bacterial genome metadata from NCBI Genome and BioSample records. FetchM links genome assemblies to their corresponding BioSample entries via the NCBI Entrez API, appends missing contextual fields, and generates summary tables and plots. The tool supports sequence filtering by user-defined criteria (e.g. year, host, country, continent) and produces ready-to-analyze datasets for downstream workflows. Results: FetchM was applied to 14 382 Availability and implementation: FetchM is licensed under MIT and is freely available at https://github.com/Tasnimul-Arabi-Anik/FetchM and PyPI.
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