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.
The most popular pipeline among respondents was Snippy with 19 mentions before custom pipelines which are used by 17. Also quite popular is the use of ParSNP on assembled genomes with 12 votes. This is slightly different from the earlier Twitter poll where 42% of 36 votes said to run a custom pipeline. The most striking thing is the diversity: there are 66 respondents and 21 different pipelines and that’s even without the custom pipelines.
Here’s a selection of reasons why the respondents use the pipeline they do:
Of course, the population that took the survey is highly biased. The use of GUI pipelines for example seems to be extremely low, which would not be the case in the average European microbiology laboratory as far as I can tell.
Thanks everyone who participated in the survey.
You can browse through the all the responses here