ArticlePloS one2018
Consensus assessment of the contamination level of publicly available cyanobacterial genomes.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- ProbeST: a custom probe design pipeline for dual host-pathogen Spatial Transcriptomics.BMC genomics · 2026Article
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
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- Decontamination of DNA sequences from a Streptomyces genome for optimal genome mining.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- Contamination Survey of Insect Genomic and Transcriptomic Data.Animals : an open access journal from MDPI · 2024Article
- Rapid and sensitive detection of genome contamination at scale with FCS-GX.Genome biology · 2024Article
- ContScout: sensitive detection and removal of contamination from annotated genomes.Nature communications · 2024Article
- GTax: improving de novo transcriptome assembly by removing foreign RNA contamination.Genome biology · 2024Article
- Ten common issues with reference sequence databases and how to mitigate them.Frontiers in bioinformatics · 2024Review
- Rapid and sensitive detection of genome contamination at scale with FCS-GX.bioRxiv : the preprint server for biology · 2023Article
- The increasing role of structural proteomics in cyanobacteria.Essays in biochemistry · 2023Review
- Trait biases in microbial reference genomes.Scientific data · 2023Article
- The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics.GigaScience · 2022Article
- Molecular characteristics of global β-lactamase-producing Enterobacter cloacae by genomic analysis.BMC microbiology · 2022Article
- Contamination detection in genomic data: more is not enough.Genome biology · 2022Review
- Review
- Beyond Nuclear Ribosomal DNA Sequences: Evolution, Taxonomy, and Closest Known Saprobic Relatives of Powdery Mildew Fungi (Frontiers in microbiology · 2022Article
- Article
- CONSULT: accurate contamination removal using locality-sensitive hashing.NAR genomics and bioinformatics · 2021Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Publicly available genomes are crucial for phylogenetic and metagenomic studies, in which contaminating sequences can be the cause of major problems. This issue is expected to be especially important for Cyanobacteria because axenic strains are notoriously difficult to obtain and keep in culture. Yet, despite their great scientific interest, no data are currently available concerning the quality of publicly available cyanobacterial genomes. As reliably detecting contaminants is a complex task, we designed a pipeline combining six methods in a consensus strategy to assess the contamination level of 440 genome assemblies of Cyanobacteria. Two methods are based on published reference databases of ribosomal genes (SSU rRNA 16S and ribosomal proteins), one is indirectly based on a reference database of marker genes (CheckM), and three are based on complete genome analysis. Among those genome-wide methods, Kraken and DIAMOND blastx share the same reference database that we derived from Ensembl Bacteria, whereas CONCOCT does not require any reference database, instead relying on differences in DNA tetramer frequencies. Given that all the six methods appear to have their own strengths and limitations, we used the consensus of their rankings to infer that >5% of cyanobacterial genome assemblies are highly contaminated by foreign DNA (i.e., contaminants were detected by 5 or 6 methods). Our results will help researchers to check the quality of publicly available genomic data before use in their own analyses. Moreover, we argue that journals should make mandatory the submission of raw read data along with genome assemblies in order to facilitate the detection of contaminants in sequence databases.
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