Mapler: A pipeline for assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads.

Bioinformatics (Oxford, England) Pub Date : 2025-06-06 DOI:10.1093/bioinformatics/btaf334

Maurice Nicolas, Claire Lemaitre, Riccardo Vicedomini, Clémence Frioux

{"title":"Mapler: A pipeline for assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads.","authors":"Maurice Nicolas, Claire Lemaitre, Riccardo Vicedomini, Clémence Frioux","doi":"10.1093/bioinformatics/btaf334","DOIUrl":null,"url":null,"abstract":"Summary: 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.Availability and implementation: 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.Supplementary information: Supplementary data are available at Bioinformatics online.","PeriodicalId":93899,"journal":{"name":"Bioinformatics (Oxford, England)","volume":" ","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Bioinformatics (Oxford, England)","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1093/bioinformatics/btaf334","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}

引用次数: 0

Abstract

Summary: 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.

Availability and implementation: 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.

Supplementary information: Supplementary data are available at Bioinformatics online.

查看原文本刊更多论文

mappler：利用HiFi reads对分类丰富的宏基因组进行测序，用于评估组装质量的管道。

摘要：宏基因组组装旨在从微生物生态系统的测序数据中重建最高质量的基因组。尽管技术进步促进了组装，例如高保真长读数，但在由数百到数千人组成的复杂环境样品中，该过程仍然具有挑战性。mappler是一个宏基因组组装和评估管道，专注于评估高保真长读宏基因组组装的质量。它结合了几个最先进的指标，以及评估组装过程中未捕获的多样性的新指标。mappler促进了组装策略的比较，并有助于确定阻碍基因组重建的方法瓶颈。可用性和实现：mappler是开源的，在AGPL-3.0许可下可在https://github.com/Nimauric/Mapler上公开获得。源代码在Python和Bash中作为蛇形管道实现。该代码的快照可在Software Heritage上获得，地址为swh:1:snp:df4f5f02e22ebbab285ec14af58d4d88436ee5d6。补充信息：补充数据可在生物信息学在线获取。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Bioinformatics (Oxford, England)

自引率

0.00%

发文量