Tuesday, 17 March 2026

Making a bubble plot to show frequencies

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I've been using ggplot2 in R to make a bubbleplot, to show frequencies. This is an alternative to a histogram. Here's a little examp...
Friday, 20 February 2026

Using MOB-suite to predict plasmids in bacterial genome assemblies

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Today I wanted to predict plasmids in a bacterial genome assembly, and used the  MOB-suite  tool. Here's how I ran it on the Sanger comp...
Thursday, 5 February 2026

Using enadownloader to download fastqs from the ENA

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I wanted to download fastq files for a long list of SRR accessions from the ENA today. I realised I could use the  enadownloader tool  that...

Making assemblies for Oxford Nanopore sequence data using Dragonflye

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I've been making genome assemblies for some Oxford Nanopore Technology (ONT) sequencing data using the  Dragonflye  package by Robert A....
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...