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LEMMI: A continuous benchmarking platform for metagenomics classifiers

By Mathieu Seppey, Mosè Manni, Evgeny M Zdobnov

Posted 28 Dec 2018
bioRxiv DOI: 10.1101/507731 (published DOI: 10.1101/gr.260398.119)

Studies of microbiomes are booming, as well as the diversity of computational tools to make sense out of the sequencing data and the volumes of accumulated microbial genotypes. LEMMI (<https://lemmi.ezlab.org>) is a novel concept of a benchmarking platform of computational tools for metagenome composition assessments that introduces: a continuous integration of tools, their multi-objective ranking, and an effective distribution through software containers. Here, we detail the workflow and discuss the evaluation of some recently released methods. 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.

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