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MaGuS: a tool for map-guided scaffolding and quality assessment of genome assemblies

Mohammed-Amin Madoui, Carole Dossat, Léo d’Agata, Jan van Oeveren, Edwin van der Vossen, Jean-Marc Aury
doi: https://doi.org/10.1101/032045
Mohammed-Amin Madoui
1CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057 Evry, France
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Carole Dossat
1CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057 Evry, France
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Léo d’Agata
1CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057 Evry, France
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Jan van Oeveren
2Keygene NV, Agro Business Park 90, 6708 PW, Wageningen, The Netherlands
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Edwin van der Vossen
2Keygene NV, Agro Business Park 90, 6708 PW, Wageningen, The Netherlands
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Jean-Marc Aury
1CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057 Evry, France
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Abstract

Background Scaffolding is a crucial step in the genome assembly process. Current methods based on large fragment paired-end reads or long reads allow an increase in continuity but often lack consistency in repetitive regions, resulting in fragmented assemblies. Here, we describe a novel tool to link assemblies to a genome map to aid complex genome reconstruction by detecting assembly errors and allowing scaffold ordering and anchoring.

Results We present MaGuS (map-guided scaffolding), a modular tool that uses a draft genome assembly, a genome map, and high-throughput paired-end sequencing data to estimate the quality and to enhance the continuity of an assembly. We generated several assemblies of the Arabidopsis genome using different scaffolding programs and applied MaGuS to select the best assembly using quality metrics. Then, we used MaGuS to perform map-guided scaffolding to increase continuity by creating new scaffold links in low-covered and highly repetitive regions where other commonly used scaffolding methods lack consistency.

Conclusions MaGuS is a powerful reference-free evaluator of assembly quality and a map-guided scaffolder that is freely available at https://github.com/institut-de-genomique/MaGuS. Its use can be extended to other high-throughput sequencing data (e.g., long-read data) and also to other map data (e.g., genetic maps) to improve the quality and the continuity of large and complex genome assemblies.

Footnotes

  • Email addresses:

    MAM: amadoui{at}genoscope.cns.fr

    CD: cdossat{at}genoscope.cns.fr

    LA: ldataga{at}genoscope.cns.fr

    EVDV: jan.van-oeveren{at}keygene.com

    JVO: edwin.van-der-vossen{at}keygene.com

    JMA: jmaury{at}genoscope.cns.fr

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted November 17, 2015.
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MaGuS: a tool for map-guided scaffolding and quality assessment of genome assemblies
Mohammed-Amin Madoui, Carole Dossat, Léo d’Agata, Jan van Oeveren, Edwin van der Vossen, Jean-Marc Aury
bioRxiv 032045; doi: https://doi.org/10.1101/032045
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MaGuS: a tool for map-guided scaffolding and quality assessment of genome assemblies
Mohammed-Amin Madoui, Carole Dossat, Léo d’Agata, Jan van Oeveren, Edwin van der Vossen, Jean-Marc Aury
bioRxiv 032045; doi: https://doi.org/10.1101/032045

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