A list of plasmid prediction tools
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In his recent publication Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data Julian Paganini reviewed software tools to predict bacterial plasmids from sequencing data.
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Published:
In his recent publication Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data Julian Paganini reviewed software tools to predict bacterial plasmids from sequencing data.
less than 1 minute read
Published:
Mobile genetic elements can be nested, like russian dolls. This is also the case for the vanA gene cluster in Enterococcus faecium, which is located on a Tn1546 transposon, which, in turn, is often located on plasmids.
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Update 2020-04-11: Now published in Bioinformatics
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mlplasmids is an R package to predict if assembled short-read contigs from E. coli, K. pneunomiae or E. faecium originated from a plasmid or a chromosome. It uses species-specific machine learning classifiers which results in high precision and accuracy. mlplasmids can be used to predict the location of, for example, antibiotic resistance genes and the plasmidome content of a population of a bacterial species. The full description of mlplasmids is available as a preprint at bioRxiv.