Identifying contamination with advanced visualization and analysis practices : metagenomic approaches for eukaryotic genome assemblies
Example uses of single-copy genes to estimate the number of bacterial genomes in an assembly (852.2Kb)
Visualization and curation of the raw tardigrade genome assembly from Koutsovoulos et al. (2016) (1.751Mb)
Summary of H. dujardini and bacterial genomes identified from the raw assembly results of Boothby et al. (2015) and Koutsovoulos et al. (2016) (31.29Kb)
Summary of functions identified by RAST in the bacterial draft genome #2 (selection #3 in Fig. 1) (373.8Kb)
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High-throughput sequencing provides a fast and cost-effective mean to recover genomes of organisms from all domains of life. However, adequate curation of the assembly results against potential contamination of non-target organisms requires advanced bioinformatics approaches and practices. Here, we re-analyzed the sequencing data generated for the tardigrade Hypsibius dujardini, and created a holistic display of the eukaryotic genome assembly using DNA data originating from two groups and eleven sequencing libraries. By using bacterial single-copy genes, k-mer frequencies, and coverage values of scaffolds we could identify and characterize multiple near-complete bacterial genomes from the raw assembly, and curate a 182 Mbp draft genome for H. dujardini supported by RNA-Seq data. Our results indicate that most contaminant scaffolds were assembled from Moleculo long-read libraries, and most of these contaminants have differed between library preparations. Our re-analysis shows that visualization and curation of eukaryotic genome assemblies can benefit from tools designed to address the needs of today’s microbiologists, who are constantly challenged by the difficulties associated with the identification of distinct microbial genomes in complex environmental metagenomes.
© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PeerJ 4 (2016): e1839, doi:10.7717/peerj.1839.
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