07 Aug 2024
Yet another Snakemake tutorial...
22 May 2024
Yet another Snakemake tutorial...
07 Jun 2022
All material for the SAGC and FAME Metagenomics Workshop for 2022 are available
from here.
21 Feb 2022
Krona plots are a fantastic way of representing heirarchial data such as taxonomic annotations.
These plots are interactive, visually appealing, and best of all they're surprisingly easy to make.
We'll use output from the metagenomics profiler 'FOCUS' as an example.
06 May 2021
I'm working on a pipeline that uses and generates tens of thousands of files,
and there's a good chance this could be expanded to produce hundreds of thousands.
I wanted to avoid creating a few folders with thousands upon thousands of files in them,
so I needed a way to distribute the files across a nested directory structure.
29 Nov 2020
We've all been there; you just want to quickly plot some data to see if an
experiment worked. You look over your shoulder to check that the coast is
clear and fire up Excel. No self respecting computer scientist would
actually use an Excel graph would they? Assuming you're happy with the
data and want something presentable, do you repeat the process in GraphPad?
Punch out a wall of R code? Or, do you just tweak it in a vector graphic
application to make it look nice?
08 Aug 2020
Following on from the previous post; in Circos part 2 I cover using ribbons to create a jupiter plot.
In this example we make the plot from a nucmer alignment (part of the MUMmer package (https://github.com/mummer4/mummer)),
using two different _Brettanomyces bruxellensis_ assemblies:
AWRI2804 (https://www.ncbi.nlm.nih.gov/assembly/GCA_011074885.1) and CBS2499 (https://www.ncbi.nlm.nih.gov/assembly/GCA_000340765.1).
The plots are great for visualising structural rearrangements and identifying potential misassemblies.
12 Jul 2020
Circos plots are a bit over-used in genomics papers and often are only there to dazzle the reader with a pretty graphic. However, they can be both useful _and_ pretty. In this part I'll cover a basic circos plot with coverage and SNP histograms, which can be helpful for things like assessing an assembly for LoH, gene conversions, redundancy, etc.
17 May 2020
If you're a data scientist/bioinformatician/whatever and are looking at making your own static website,
you can't go wrong with GitHub Pages (https://pages.github.com).
It's free, it's easy, and it's fast. There are plenty of tutorials on the subject and I'm not an expert,
so, this is not a guide, just a breif showcase.