Maurice Nicolas, Lemaitre Claire, Vicedomini Riccardo, Frioux Clémence
Univ Rennes, Inria, CNRS, IRISA - UMR 6074, F-35000 Rennes, France.
Inria, University of Bordeaux, INRAE, F-33400 Talence, France.
Bioinformatics. 2025 Jun 2;41(6). doi: 10.1093/bioinformatics/btaf334.
Metagenome assembly seeks to reconstruct the most high-quality genomes from sequencing data of microbial ecosystems. Despite technological advancements that facilitate assembly, such as Hi-Fi long reads, the process remains challenging in complex environmental samples consisting of hundreds to thousands of populations. Mapler is a metagenome assembly and evaluation pipeline with a focus on evaluating the quality of Hi-Fi long read metagenome assemblies. It incorporates several state-of-the-art metrics, as well as novel metrics assessing the diversity that remains uncaptured by the assembly process. Mapler facilitates the comparison of assembly strategies and helps identify methodological bottlenecks that hinder genome reconstruction.
Mapler is open source and publicly available under the AGPL-3.0 licence at https://github.com/Nimauric/Mapler. Source code is implemented in Python and Bash as a Snakemake pipeline. A snapshot of the code is available on Software Heritage at swh:1:snp:df4f5f02e22ebbab285ec14af58d4d88436ee5d6. Raw data and results are available at https://entrepot.recherche.data.gouv.fr/dataset.xhtml?persistentId=doi:10.57745/2SA8AB.
宏基因组组装旨在从微生物生态系统的测序数据中重建质量最高的基因组。尽管诸如高保真长读长等技术进步有助于组装，但在由数百到数千个种群组成的复杂环境样本中，该过程仍然具有挑战性。Mapler是一个宏基因组组装和评估流程，重点是评估高保真长读长宏基因组组装的质量。它纳入了几个最新的指标，以及评估组装过程中未捕获的多样性的新指标。Mapler有助于比较组装策略，并有助于识别阻碍基因组重建的方法瓶颈。
Mapler是开源的，根据AGPL-3.0许可在https://github.com/Nimauric/Mapler上公开提供。源代码用Python和Bash作为Snakemake流程实现。代码的快照可在Software Heritage上获取，链接为swh:1:snp:df4f5f02e22ebbab285ec14af58d4d88436ee5d6。原始数据和结果可在https://entrepot.recherche.data.gouv.fr/dataset.xhtml?persistentId=doi:10.57745/2SA8AB上获取。
