Alternative bioinformatics

By Grant Jacobs 04/07/2013

There’s alternative ‘medicine’, then there’s alternative bioinformatics.

Those who aren’t computational biologists / bioinformaticists should proceed no further. You really won’t get these, they’re way too in-house. You really need do to know something of the tools to make sense of them. But that’s also the beauty of it.

I’ve just selected a few, more-or-less in chronological order; check the original source for more. As you can see we owe this to Mick Watson (get past the first few, they’re to introduce theme):

After my shamtools tweet yesterday, I’m going to start a new hashtag:

Shamtools: software that pretends to do everything Samtools does, but actually does nothing

BEDRules: software that encourages you to go to bed every time you try and figure out which command in BEDTools you need

NoTie: the aligner that just prints NO

TooPHat: the splice aware aligner for when your data set is just PHAT

REMEMBOSS: software utility that periodically reminds you of the existence of EMBOSS

WHAMtools: a tool for converting sequence to 80s pop music

IntoTheABySS de novo assembly tool that organizes your contigs by circles of hell (see Dante’s Inferno)

n00bler: Assembler which takes input in Microsoft Word format

SPMMER: hidden Markov models to ascertain what’s really in dubious tinned meat products

PhyloPithier: attempts to assign metagenomic data to taxons then makes a sarcastic remark about how badly it performed

BASTA : a new structured format storing infinite amount of sequences without any way to retrieve them

GeeGeeplot: Equestrian images R package

ARRR: Statistical package for pirates.

. MUMmYer: sequence aligner for samples of long-dead humans.

and my own rather feeble contribution,

Cn3D – sensibly displays a rotating letter C

Other articles on Code for life:

Who has the most bioinformatics scientists? | Code for Life – SciBlogs

External (bioinformatics) specialists: best on the grant from the onset …

Retrospective–The mythology of bioinformatics | Code for Life

Developing bioinformatics methods: by who and how | Code for Life

Friday picture: molecular modelling of the cytoplasm

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