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

hal.structure.identifierScalable, Optimized and Parallel Algorithms for Genomics [GenScale]
hal.structure.identifierPleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
dc.contributor.authorMAURICE, Nicolas
hal.structure.identifierScalable, Optimized and Parallel Algorithms for Genomics [GenScale]
dc.contributor.authorLEMAITRE, Claire
hal.structure.identifierScalable, Optimized and Parallel Algorithms for Genomics [GenScale]
hal.structure.identifierInstitut des sciences informatiques et de leurs interactions - CNRS Sciences informatiques [INS2I-CNRS]
dc.contributor.authorVICEDOMINI, Riccardo
hal.structure.identifierPleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
dc.contributor.authorFRIOUX, Clémence
dc.date.issued2025-06-02
dc.identifier.issn1367-4803
dc.description.abstractEnAbstract 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. Raw data and results are available at https://entrepot.recherche.data.gouv.fr/dataset.xhtml?persistentId=doi:10.57745/2SA8AB.
dc.description.sponsorshipComputationel models of crop plant microbial biodiversity - ANR-22-PEAE-0011
dc.language.isoen
dc.publisherOxford University Press (OUP)
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subject.enSequance analysis
dc.subject.enSequence alignment
dc.subject.enMicrobiome
dc.subject.enMetagenomics
dc.subject.enSoftware
dc.subject.enMetagenome assembly
dc.subject.enHiFi long reads
dc.subject.enComplex microbial ecosystems
dc.subject.enBenchmarking
dc.subject.enEvaluation
dc.subject.enBioinformatics
dc.title.enMapler: a pipeline for assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads
dc.typeArticle de revue
dc.identifier.doi10.1093/bioinformatics/btaf334
dc.subject.halInformatique [cs]/Bio-informatique [q-bio.QM]
bordeaux.journalBioinformatics
bordeaux.volume41
bordeaux.issue6
bordeaux.peerReviewedoui
hal.identifierhal-05288241
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-05288241v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Bioinformatics&rft.date=2025-06-02&rft.volume=41&rft.issue=6&rft.eissn=1367-4803&rft.issn=1367-4803&rft.au=MAURICE,%20Nicolas&LEMAITRE,%20Claire&VICEDOMINI,%20Riccardo&FRIOUX,%20Cl%C3%A9mence&rft.genre=article


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