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<p>Metagenomics enables culture-independent investigation of microbial communities without prior knowledge of sample composition. However, sequence analysis is complex, and many computational strategies exist. Selecting among them is challenging, and novel tools face visibility issues. Here, we present LEMMIv2, an updated platform for continuous benchmarking of metagenomic profilers, providing developers with impartial benchmarks and offering users a catalogue of evaluated tools. New features include support for alternative taxonomies and long-read applications, and a standalone pipeline for local benchmarking. We also extend the approach to 16S amplicon profiling with LEMMI16S, which evaluates methods across several reference databases.</p>

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LEMMIv2: benchmarking framework for metagenomic and 16S amplicon profilers with a catalogue of evaluated tools

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年4月28日

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  • Mathieu Seppey,
  • Andres Benavides,
  • Matthew R. Berkeley,
  • Mosè Manni,
  • Evgeny M. Zdobnov

摘要

Metagenomics enables culture-independent investigation of microbial communities without prior knowledge of sample composition. However, sequence analysis is complex, and many computational strategies exist. Selecting among them is challenging, and novel tools face visibility issues. Here, we present LEMMIv2, an updated platform for continuous benchmarking of metagenomic profilers, providing developers with impartial benchmarks and offering users a catalogue of evaluated tools. New features include support for alternative taxonomies and long-read applications, and a standalone pipeline for local benchmarking. We also extend the approach to 16S amplicon profiling with LEMMI16S, which evaluates methods across several reference databases.