bowtie2: Relaxed Parameters for Generous Alignments to Metagenomes

   Sam Nicholls    No Comments yet    Tools

Even `bowtie2`’s `–very-sensitive-local` option can be a little grumpy. Here’s how I make `bowtie2` a little more relaxed for alignment of more dissimilar sequences, particularly for my work on metagenomes.


Bioinformatics is a disorganised disaster and I am too. So I made a shell.

   Sam Nicholls    No Comments yet    Bioinformatics, chitin

I am not a very organised bioinformatician, and despite your best efforts, you probably aren’t either. I’ve written a tool called `chitin` that tries to keep me, and bioinformatics more organised.


A pretend biologist’s guide to running a PCR (polymerase chain reaction)

   Sam Nicholls    No Comments yet    Protocol Guides

I wrote a PCR (polymerase chain reaction) protocol for somebody who has never held a pipette before. Prepare to spend all day pipetting colourless liquids into a tube, only to find that it all didn’t work anyway.


An idiot’s guide to Python documentation with Sphinx and ReadTheDocs

   Sam Nicholls    No Comments yet    Documentation, Python

This is the third occasion that I’ve come to set up a Python package’s documentation. It is also the third occasion where I’ve spent many hours and commits trying to work out how I made everything work last time. So for my future sanity and possibly yours, here’s a quick guide on setting up Sphinx-based, ReadTheDocs-hosted Python documentation.