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ABPHM17

Poster ABPHM17

less than 1 minute read

Published:

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

E. coli

Plasmid genomics: gplas

less than 1 minute read

Published:

gplas is a software tool to find different plasmids in short read sequenced bacterial genomes. It bins contigs that are predicted as plasmids into separate entities, corresponding to different plasmids. To do that, it uses kmer information to determine plasmid nodes, then it makes use of the nformation in the assembly graph, i.e. the connectivity of the nodes and finally it takes the coverage of the separate nodes into account. It works best in combination with the prediction of mlplasmids, thus with species-specific models for classification, but it can also use plasflow which has a species-independent model for classification.

mlplasmids FAQ

2 minute read

Published:

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.

E. faecium

Plasmid genomics: gplas

less than 1 minute read

Published:

gplas is a software tool to find different plasmids in short read sequenced bacterial genomes. It bins contigs that are predicted as plasmids into separate entities, corresponding to different plasmids. To do that, it uses kmer information to determine plasmid nodes, then it makes use of the nformation in the assembly graph, i.e. the connectivity of the nodes and finally it takes the coverage of the separate nodes into account. It works best in combination with the prediction of mlplasmids, thus with species-specific models for classification, but it can also use plasflow which has a species-independent model for classification.

mlplasmids FAQ

2 minute read

Published:

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.

K. pneumoniae

Plasmid genomics: gplas

less than 1 minute read

Published:

gplas is a software tool to find different plasmids in short read sequenced bacterial genomes. It bins contigs that are predicted as plasmids into separate entities, corresponding to different plasmids. To do that, it uses kmer information to determine plasmid nodes, then it makes use of the nformation in the assembly graph, i.e. the connectivity of the nodes and finally it takes the coverage of the separate nodes into account. It works best in combination with the prediction of mlplasmids, thus with species-specific models for classification, but it can also use plasflow which has a species-independent model for classification.

mlplasmids FAQ

2 minute read

Published:

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.

R

mlplasmids FAQ

2 minute read

Published:

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.

Drawing a tree with colored tips in R (ggtree)

1 minute read

Published:

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.

SNP pipelines

Popularity of SNP pipelines

2 minute read

Published:

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.

assembly graph

Plasmid genomics: gplas

less than 1 minute read

Published:

gplas is a software tool to find different plasmids in short read sequenced bacterial genomes. It bins contigs that are predicted as plasmids into separate entities, corresponding to different plasmids. To do that, it uses kmer information to determine plasmid nodes, then it makes use of the nformation in the assembly graph, i.e. the connectivity of the nodes and finally it takes the coverage of the separate nodes into account. It works best in combination with the prediction of mlplasmids, thus with species-specific models for classification, but it can also use plasflow which has a species-independent model for classification.

bioinformatics

Plasmid genomics: gplas

less than 1 minute read

Published:

gplas is a software tool to find different plasmids in short read sequenced bacterial genomes. It bins contigs that are predicted as plasmids into separate entities, corresponding to different plasmids. To do that, it uses kmer information to determine plasmid nodes, then it makes use of the nformation in the assembly graph, i.e. the connectivity of the nodes and finally it takes the coverage of the separate nodes into account. It works best in combination with the prediction of mlplasmids, thus with species-specific models for classification, but it can also use plasflow which has a species-independent model for classification.

mlplasmids FAQ

2 minute read

Published:

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.

Popularity of SNP pipelines

2 minute read

Published:

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.

Poster ABPHM17

less than 1 minute read

Published:

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

Drawing a tree with colored tips in R (ggtree)

1 minute read

Published:

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.

chromosome

Plasmid genomics: gplas

less than 1 minute read

Published:

gplas is a software tool to find different plasmids in short read sequenced bacterial genomes. It bins contigs that are predicted as plasmids into separate entities, corresponding to different plasmids. To do that, it uses kmer information to determine plasmid nodes, then it makes use of the nformation in the assembly graph, i.e. the connectivity of the nodes and finally it takes the coverage of the separate nodes into account. It works best in combination with the prediction of mlplasmids, thus with species-specific models for classification, but it can also use plasflow which has a species-independent model for classification.

mlplasmids FAQ

2 minute read

Published:

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.

data carpentry

first post

Drawing a tree with colored tips in R (ggtree)

1 minute read

Published:

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.

ggtree

Drawing a tree with colored tips in R (ggtree)

1 minute read

Published:

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.

gplas

Plasmid genomics: gplas

less than 1 minute read

Published:

gplas is a software tool to find different plasmids in short read sequenced bacterial genomes. It bins contigs that are predicted as plasmids into separate entities, corresponding to different plasmids. To do that, it uses kmer information to determine plasmid nodes, then it makes use of the nformation in the assembly graph, i.e. the connectivity of the nodes and finally it takes the coverage of the separate nodes into account. It works best in combination with the prediction of mlplasmids, thus with species-specific models for classification, but it can also use plasflow which has a species-independent model for classification.

machine learning

mlplasmids FAQ

2 minute read

Published:

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.

microbial

Popularity of SNP pipelines

2 minute read

Published:

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.

mlplasmids

mlplasmids FAQ

2 minute read

Published:

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.

phylogeny

Drawing a tree with colored tips in R (ggtree)

1 minute read

Published:

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.

plasmid

Plasmid genomics: gplas

less than 1 minute read

Published:

gplas is a software tool to find different plasmids in short read sequenced bacterial genomes. It bins contigs that are predicted as plasmids into separate entities, corresponding to different plasmids. To do that, it uses kmer information to determine plasmid nodes, then it makes use of the nformation in the assembly graph, i.e. the connectivity of the nodes and finally it takes the coverage of the separate nodes into account. It works best in combination with the prediction of mlplasmids, thus with species-specific models for classification, but it can also use plasflow which has a species-independent model for classification.

mlplasmids FAQ

2 minute read

Published:

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.

Poster ABPHM17

less than 1 minute read

Published:

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

podcast

Plasmid genomics: gplas

less than 1 minute read

Published:

gplas is a software tool to find different plasmids in short read sequenced bacterial genomes. It bins contigs that are predicted as plasmids into separate entities, corresponding to different plasmids. To do that, it uses kmer information to determine plasmid nodes, then it makes use of the nformation in the assembly graph, i.e. the connectivity of the nodes and finally it takes the coverage of the separate nodes into account. It works best in combination with the prediction of mlplasmids, thus with species-specific models for classification, but it can also use plasflow which has a species-independent model for classification.

poster

Poster ABPHM17

less than 1 minute read

Published:

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

teaching

tuberculosis

twitter

Popularity of SNP pipelines

2 minute read

Published:

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.

visualization

Drawing a tree with colored tips in R (ggtree)

1 minute read

Published:

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.

workflows