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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.
Here’s the poster presented by Sergio Arredondo Alonso at the 5th International Conference on Enterococci in Chamonix, FR.
Recently we got back a round of reviews on a small review paper. There was one sentence in the text were I listed some SNP pipelines that I thought were good examples. The topic of the review is not pipelines so the intention was not to list all, just one or two. However reviewer 2 did not agree with my choice of examples. He suggested to omit the name of the pipeline that was unpublished and name a few other published ones instead.
Here’s the poster presented at ‘Applied Bioinformatics and Public Health Microbiology 2017’ at the Wellcome Genome Campus, Hinxton, Cambridge, UK on the Enterococcus faecium plasmidome
ggtree is a R package designed for viewing and annotating phylogenetic trees. It is based on the ggplot2 package. Here I will show step-by-step how to draw a tree with colored tips, because, even thought the bioconductor documentation is clear and complete, I did not read about this very common visualization.