SeqAfrica: Bioinformatics Tool Selection for AMR Surveillance in Africa

SeqAfrica project evaluated over 80 bioinformatics tools for decentralized antimicrobial resistance genomic surveillance in Africa. The evaluation focused on usability, cost, accessibility, and AMR relevance for Oxford Nanopore Technologies sequencing data. The findings were authored by Niamh Lacy-Roberts and published on figshare in April 2026.

Use Cases

• Selecting user-friendly bioinformatics tools for AMR surveillance based on usability and accessibility criteria mentioned in the description
• Evaluating tool interoperability and scalability for local infrastructure based on the assessment of Terra.bio and EPI2ME
• Developing standardized, offline-capable workflows for genomic analysis based on the pilot implementation of EPI2ME-based workflows

Strengths

• Evaluated over 80 bioinformatics tools, providing a broad comparison.
• Focus on graphical user interface tools for non-bioinformatician use, addressing a specific user need.
• Clear identification of leading candidates (Terra.bio and EPI2ME) with stated strengths.

Limitations

• The dataset is a 61.1 KB DOCX file, suggesting limited scope and likely a summary document rather than raw data.
• Row count and column-level documentation are absent; data structure must be inferred after download.
• The description is a project summary; the actual data quality and content require manual inspection.

Provenance

Source

figshare

Collection Method

Tool evaluation via two surveys and an expert elicitation workshop.

Freshness

Last updated 2026-04-09 05:20:12

Geography

Africa