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Finishing bacterial genome assemblies with Mix

hal.structure.identifierNetherlands Cancer Institute
dc.contributor.authorSOUEIDAN, Hayssam
hal.structure.identifierCentre de Bioinformatique de Bordeaux
dc.contributor.authorMAURIER, Florence
hal.structure.identifierCentre de Bioinformatique de Bordeaux
dc.contributor.authorGROPPI, Alexis
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorSIRAND-PUGNET, Pascal
hal.structure.identifierAgence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail [ANSES]
dc.contributor.authorTARDY, Florence
hal.structure.identifierInteractions hôtes-agents pathogènes [Toulouse] [IHAP]
hal.structure.identifierUniversité Toulouse III - Paul Sabatier [UT3]
dc.contributor.authorCITTI, Christine
hal.structure.identifierContrôle des maladies animales exotiques et émergentes [UMR CMAEE]
dc.contributor.authorDUPUY, Virginie
hal.structure.identifierLaboratoire Bordelais de Recherche en Informatique [LaBRI]
hal.structure.identifierCentre de Bioinformatique de Bordeaux
dc.contributor.authorNIKOLSKI, Macha
dc.date.issued2013
dc.date.conference2013-10-17
dc.description.abstractEnMotivation: Among challenges that hamper reaping the benefits of genome assembly are both unfinished assemblies and the ensuing experimental costs. First, numerous software solutions for genome de novo assembly are available, each having its advantages and drawbacks, without clear guidelines as to how to choose among them. Second, these solutions produce draft assemblies that often require a resource intensive finishing phase. Methods: In this paper we address these two aspects by developing Mix, a tool that mixes two or more draft assemblies, without relying on a reference genome and having the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a set of paths in the extension graph that maximizes the cumulative contig length. Results: We evaluate the performance of Mix on bacterial NGS data from the GAGE-B study and apply it to newly sequenced Mycoplasma genomes. Resulting final assemblies demonstrate a significant improvement in the overall assembly quality. In particular, Mix is consistent by providing better overall quality results even when the choice is guided solely by standard assembly statistics, as is the case for de novo projects. Availability: Mix is implemented in Python and is available at https://github.com/cbib/MIX, novel data for our Mycoplasma study is available at http://services.cbib.u-bordeaux2.fr/mix/.
dc.language.isoen
dc.publisherBioMed Central Ltd
dc.publisher.locationLondres (united kingdom)
dc.source.titleBMC Bioinformatics
dc.title.enFinishing bacterial genome assemblies with Mix
dc.typeCommunication dans un congrès
dc.identifier.doi10.1186/1471-2105-14-S15-S16
dc.subject.halSciences du Vivant [q-bio]
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale
bordeaux.volume14 (suppl. 15)
bordeaux.conference.title11. Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics
bordeaux.countryFR
bordeaux.title.proceedingBMC Bioinformatics
bordeaux.conference.cityLyon
bordeaux.peerReviewedoui
hal.identifierhal-02749841
hal.version1
hal.invitednon
hal.conference.organizerInstitut National de Recherche en Informatique et en Automatique (INRIA). FRA.
hal.conference.end2013-10-19
hal.popularnon
hal.audienceNationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02749841v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.btitle=BMC%20Bioinformatics&rft.date=2013&rft.volume=14%20(suppl.%2015)&rft.au=SOUEIDAN,%20Hayssam&MAURIER,%20Florence&GROPPI,%20Alexis&SIRAND-PUGNET,%20Pascal&TARDY,%20Florence&rft.genre=unknown


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