Evidence map›Paper›PMID 42050730›Full record

ArticleGenome biology2026

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

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

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Mathieu Seppey *Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, Geneva, Switzerland.
Andres Benavides *Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, Geneva, Switzerland.
Matthew R BerkeleyDepartment of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, Geneva, Switzerland.
Mosè ManniDepartment of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, Geneva, Switzerland.
Evgeny M ZdobnovDepartment of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, Geneva, Switzerland. evgeny.zdobnov@unige.ch.

Funding

Federal Commission for Scholarships for Foreign Students for the Swiss Government Excellence Scholarship ESKAS No. 2022.0531Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung 310030_189062
6 · The paper itself

Abstract

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.

Indexed as

MetagenomicsRNA, Ribosomal, 16SSoftwareBenchmarkingRNA, Ribosomal, 16S

Identifiers

PMID42050730
PMCPMC13270737

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.