Mapler: a pipeline for assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads
| hal.structure.identifier | Scalable, Optimized and Parallel Algorithms for Genomics [GenScale] | |
| hal.structure.identifier | Pleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE] | |
| dc.contributor.author | MAURICE, Nicolas | |
| hal.structure.identifier | Scalable, Optimized and Parallel Algorithms for Genomics [GenScale] | |
| dc.contributor.author | LEMAITRE, Claire | |
| hal.structure.identifier | Scalable, Optimized and Parallel Algorithms for Genomics [GenScale] | |
| hal.structure.identifier | Institut des sciences informatiques et de leurs interactions - CNRS Sciences informatiques [INS2I-CNRS] | |
| dc.contributor.author | VICEDOMINI, Riccardo | |
| hal.structure.identifier | Pleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE] | |
| dc.contributor.author | FRIOUX, Clémence | |
| dc.date.issued | 2025-06-02 | |
| dc.identifier.issn | 1367-4803 | |
| dc.description.abstractEn | 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. Raw data and results are available at https://entrepot.recherche.data.gouv.fr/dataset.xhtml?persistentId=doi:10.57745/2SA8AB. | |
| dc.description.sponsorship | Computationel models of crop plant microbial biodiversity - ANR-22-PEAE-0011 | |
| dc.language.iso | en | |
| dc.publisher | Oxford University Press (OUP) | |
| dc.rights.uri | http://creativecommons.org/licenses/by/ | |
| dc.subject.en | Sequance analysis | |
| dc.subject.en | Sequence alignment | |
| dc.subject.en | Microbiome | |
| dc.subject.en | Metagenomics | |
| dc.subject.en | Software | |
| dc.subject.en | Metagenome assembly | |
| dc.subject.en | HiFi long reads | |
| dc.subject.en | Complex microbial ecosystems | |
| dc.subject.en | Benchmarking | |
| dc.subject.en | Evaluation | |
| dc.subject.en | Bioinformatics | |
| dc.title.en | Mapler: a pipeline for assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads | |
| dc.type | Article de revue | |
| dc.identifier.doi | 10.1093/bioinformatics/btaf334 | |
| dc.subject.hal | Informatique [cs]/Bio-informatique [q-bio.QM] | |
| bordeaux.journal | Bioinformatics | |
| bordeaux.volume | 41 | |
| bordeaux.issue | 6 | |
| bordeaux.peerReviewed | oui | |
| hal.identifier | hal-05288241 | |
| hal.version | 1 | |
| hal.popular | non | |
| hal.audience | Internationale | |
| hal.origin.link | https://hal.archives-ouvertes.fr//hal-05288241v1 | |
| bordeaux.COinS | ctx_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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