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LEMMI: a continuous benchmarking platform for metagenomics classifiers

Published in Genome Research. 2020
Abstract Studies of microbiomes are booming, along with the diversity of computational approaches to make sense out of the sequencing data and the volumes of accumulated microbial genotypes. A swift evaluation of newly published methods and their improvements against established tools is necessary to reduce the time between the method's release and its adoption in microbiome analyses. The LEMMI platform offers a novel approach for benchmarking software dedicated to metagenome composition assessments based on read classification. It enables the integration of newly published methods in an independent and centralized benchmark designed to be continuously open to new submissions. This allows developers to be proactive regarding comparative evaluations and guarantees that any promising methods can be assessed side-by-side with established tools quickly after their release. Moreover, LEMMI enforces an effective distribution through software containers to ensure long term availability of all methods. Here, we detail the LEMMI workflow and discuss the performances of some previously unevaluated tools. We see this platform eventually as a community-driven effort where method developers can showcase novel approaches and get unbiased benchmarks for publications, while users can make informed choices and obtain standardized and easy-to-use tools.
PMID: 32616517
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Research group Génomique Evolutionnaire Computationnelle (830)
Swiss National Science Foundation: 31003A_166483
Swiss National Science Foundation: 310030_189062
(ISO format)
SEPPEY, Mathieu, MANNI, Mose, ZDOBNOV, Evgeny. LEMMI: a continuous benchmarking platform for metagenomics classifiers. In: Genome Research, 2020. doi: 10.1101/gr.260398.119 https://archive-ouverte.unige.ch/unige:139248

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Deposited on : 2020-08-11

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