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.