LEMMI: A continuous benchmarking platform for metagenomics classifiers

Mathieu Seppey, Mose Manni, Evgeny M Zdobnov
2020 Genome Research  
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
more » ... d 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.
doi:10.1101/gr.260398.119 pmid:32616517 pmcid:PMC7462069 fatcat:yayqy443enelzjmrndog7rhp2y