Wednesday, 6 May 2026

The Perceptron - classifying items into two classes based on numerical input variables

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I've been reading Sebastian Raschka's excellent book Machine Learning with PyTorch and Scikit-Learn  about machine learning/AI using...
Tuesday, 28 April 2026

Installing Python libraries within virtualenv

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 Today I learnt how to install Python libraries in a virtual environment (in my case, on the Sanger compute farm), using  virtualenv .  Here...
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...