ArticlePeerJ2016
Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies.
Article in PeerJ, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed, 114 citations in OpenAlex.
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- Genomic characterisation and ecological distribution ofFrontiers in microbiology · 2024Article
- Shaping eukaryotic epigenetic systems by horizontal gene transfer.BioEssays : news and reviews in molecular, cellular and developmental biology · 2023Article
- Metabolic independence drives gut microbial colonization and resilience in health and disease.Genome biology · 2023Article
- Mirusviruses link herpesviruses to giant viruses.Nature · 2023Article
- Increasing temperature-driven changes in life history traits and gene expression of an Antarctic tardigrade species.Frontiers in physiology · 2023Article
- Deciphering the Biological Enigma-Genomic Evolution Underlying Anhydrobiosis in the Phylum Tardigrada and the ChironomidInsects · 2022Review
- Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean.Cell genomics · 2022Article
- Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean.The ISME journal · 2022Article
- Bacterial N4-methylcytosine as an epigenetic mark in eukaryotic DNA.Nature communications · 2022Article
- Contamination detection in genomic data: more is not enough.Genome biology · 2022Review
- Tiara: deep learning-based classification system for eukaryotic sequences.Bioinformatics (Oxford, England) · 2022Article
- Gut Microbiota Linked with Reduced Fear of Humans in Red Junglefowl Has Implications for Early Domestication.Advanced genetics (Hoboken, N.J.) · 2021Article
- Accurate annotation of protein coding sequences with IDTAXA.NAR genomics and bioinformatics · 2021Article
- Discovery of Viral Myosin Genes With Complex Evolutionary History Within Plankton.Frontiers in microbiology · 2021Article
- Microbial Ecology of Oxygen Minimum Zones Amidst Ocean Deoxygenation.Frontiers in microbiology · 2021Review
- Genome Survey Sequencing of In Vivo Mother Plant and In Vitro Plantlets ofPlants (Basel, Switzerland) · 2020Article
- Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota.Scientific data · 2020Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.