Finishing bacterial genome assemblies with Mix

Soueidan Hayssam, Maurier Florence, Groppi Alexis, Sirand-Pugnet Pascal, Tardy Florence, Citti Christine, Dupuy Virginie, Nikolskii G.V.. 2013. Finishing bacterial genome assemblies with Mix. BMC Bioinformatics, 14 (15), suppl., 11 p. Annual Research in Computational Molecular Biology. 11, Lyon, France, 17 Octobre 2013/19 Octobre 2013.

Quartile : Q1, Sujet : MATHEMATICAL & COMPUTATIONAL BIOLOGY / Quartile : Q2, Sujet : BIOTECHNOLOGY & APPLIED MICROBIOLOGY / Quartile : Q2, Sujet : BIOCHEMICAL RESEARCH METHODS

Résumé : Motivation 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.

Classification Agris : U10 - Informatique, mathématiques et statistiques
H20 - Maladies des plantes

Champ stratégique Cirad : Axe 1 (2005-2013) - Intensification écologique

Auteurs et affiliations

• Soueidan Hayssam, Netherlands Cancer Institute (NLD)
• Maurier Florence, Université de Bordeaux II (FRA)
• Groppi Alexis, Université de Bordeaux II (FRA)
• Sirand-Pugnet Pascal, INRA (FRA)
• Tardy Florence, ANSES (FRA)
• Citti Christine, ENVT (FRA)
• Dupuy Virginie, CIRAD-BIOS-UMR CMAEE (FRA)
• Nikolskii G.V., Université de Bordeaux II (FRA)

Source : Cirad - Agritrop (https://agritrop.cirad.fr/571318/)

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