Monday, 17 November 2025

Making a map of the locations where bacterial isolates were collected

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 I wanted to make a map of the locations in the world were some bacterial isolates were collected. I found a  nice website  that gave me som...
Friday, 14 November 2025

Submitting V. cholerae and MLST sequence types to PubMLST

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 I've been submitting novel Vibrio cholerae MLST alleles and sequence types to the  PubMLST  database. This is the  website for submitti...
Friday, 10 January 2025

Using snippy to find SNPs in bacterial genomes

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I have been learning how to use snippy by Torsten Seemann to identify SNPs in bacterial genomes. Running snippy To run snippy on the Sanger...
Thursday, 22 August 2024

Using an image that has a Creative Commons license

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 I'm writing some online training material, and want to include some images that have Creative Commons licenses, so need to figure out h...
Monday, 17 June 2024

Making documentation on readthedocs

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I've found the Readthedocs website really useful for making documentation, for example, for the Little Books of R and for the Vibriowa...
Thursday, 16 May 2024

Testing whether data follow a uniform distribution

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Someone asked me how to test whether a data variable, which has values ranging from 1-1000, follows a uniform distribution.  Getting some in...
Thursday, 2 May 2024

Finding SNPs in a core gene alignment using snp-sites

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Today I'm using the snp-sites software (by Page et al 2016 ) to extract SNPs from core gene alignments (output from Panaroo ). It's...