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LEMMI:用于宏基因组分类器的连续基准测试平台。

LEMMI: a continuous benchmarking platform for metagenomics classifiers.

机构信息

Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland.

出版信息

Genome Res. 2020 Aug;30(8):1208-1216. doi: 10.1101/gr.260398.119. Epub 2020 Jul 2.


DOI:10.1101/gr.260398.119
PMID:32616517
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7462069/
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 methods' release and their 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 in which method developers can showcase novel approaches and get unbiased benchmarks for publications, and users can make informed choices and obtain standardized and easy-to-use tools.

摘要

微生物组的研究正在蓬勃发展,与此同时,用于从测序数据中获取有意义信息的计算方法的多样性,以及积累的微生物基因型的数量也在不断增加。为了缩短方法发布到在微生物组分析中采用之间的时间,有必要快速评估新发布的方法及其对现有工具的改进。LEMMI 平台提供了一种新颖的方法,用于基于读取分类对专门用于宏基因组组成评估的软件进行基准测试。它能够将新发布的方法集成到一个独立的、集中的基准测试中,该基准测试旨在持续开放新的提交。这使开发人员能够主动进行比较评估,并确保在发布后能够快速与现有工具一起评估任何有前途的方法。此外,LEMMI 通过软件容器强制实现有效的分发,以确保所有方法的长期可用性。在这里,我们详细介绍了 LEMMI 工作流程,并讨论了一些以前未评估工具的性能。我们最终希望将这个平台视为一个社区驱动的努力,在这个平台上,方法开发人员可以展示新的方法,并为出版物获得公正的基准测试,用户可以做出明智的选择,并获得标准化且易于使用的工具。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c31a/7462069/824766de6af6/1208f03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c31a/7462069/1224905c6a2c/1208f01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c31a/7462069/8c5ff53509bc/1208f02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c31a/7462069/824766de6af6/1208f03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c31a/7462069/1224905c6a2c/1208f01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c31a/7462069/8c5ff53509bc/1208f02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c31a/7462069/824766de6af6/1208f03.jpg

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本文引用的文献

[1]
ganon: precise metagenomics classification against large and up-to-date sets of reference sequences.

Bioinformatics. 2020-7-1

[2]
CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data.

Genome Biol. 2020-4-28

[3]
A complete domain-to-species taxonomy for Bacteria and Archaea.

Nat Biotechnol. 2020-4-27

[4]
Improved metagenomic analysis with Kraken 2.

Genome Biol. 2019-11-28

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Cell. 2019-8-8

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Nat Commun. 2019-3-27

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Genome Biol. 2019-3-4

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Genome Biol. 2019-2-27

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[10]
Why rankings of biomedical image analysis competitions should be interpreted with care.

Nat Commun. 2018-12-6

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