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Poster Communications Year : 2018

Reference guided genome assembly in metagenomic samples

Abstract

Metagenomic sequencing is a promising way to reconstruct genomes of a large diversity of bacterial species in their environment. To reconstruct the genome of a single interest species, current approaches require the metagenomic assembly of the whole community. This method appears to be computationally unnecessarily intensive, and error prone, in particular when closely related species are present, as highlighted by the results of the CAMI challenge (Sczyrba2017). A solution to enable targeting genome assembly from metagenomic samples is to use the information of a reference genome as a backbone for the assembly. However, among the existing reference-guided assembly softwares, none takes into account the specificities of metagenomic data, including high volume and heterogeneous genotypes. In this work, we propose a two-step reference-guided assembly method tailored for metagenomic data. First, a subset of the reads belonging to the species of interest are recruited by mapping and assembled into backbone contigs. The gapfiller MindTheGap is then used to perform an all-versus-all contig gapfilling and assemble the missing regions between the backbone contigs, which are regions different from the reference genome. MindTheGap algorithm makes no assumption on the synteny of backbone contigs, the potential structural variations within the sample, or the length of the missing regions. The result of the method is a genome assembly graph in gfa format, accounting for the structure of assembled genome, including the potential structural variations identified within the sample. This hybrid approach does not require a closely related reference and yet enables the targeted assembly of a species of interest from potentially large metagenomic read sets. This approach was applied in the context of the pea aphid microbiome and outperformed several alternative strategies. Starting from a remote reference genome, we were able to assemble the full circular sequence of Buchnera aphidicola, symbiont of the pea aphid. MindTheGap was also able to assemble full circular sequences of APSE bacteriophages, including coexisting strains within the same read sample differing by large structural variants, such as novel virulence cassettes of several kilobases.
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Dates and versions

hal-01934823 , version 1 (26-11-2018)

Identifiers

  • HAL Id : hal-01934823 , version 1

Cite

Cervin Guyomar, Wesley Delage, Fabrice Legeai, Christophe Mougel, Jean-Christophe Simon, et al.. Reference guided genome assembly in metagenomic samples. RECOMB 2018 - 22nd International Conference on Research in Computational Molecular Biology, Apr 2018, Paris, France. pp.1. ⟨hal-01934823⟩
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