Alternative bioinformatics
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: #altbioinf
Shamtools: software that pretends to do everything Samtools does, but actually does nothing #altbioinf
BEDRules: software that encourages you to go to bed every time you try and figure out which command in BEDTools you need #altbioinf
@BioMickWatson NoTie: the aligner that just prints NO #altbioinf
@BioMickWatson TooPHat: the splice aware aligner for when your data set is just PHAT #altbioinf
REMEMBOSS: software utility that periodically reminds you of the existence of EMBOSS #altbioinf
WHAMtools: a tool for converting sequence to 80s pop music #altbioinf
@BioMickWatson 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 #altbioinf
SPMMER: hidden Markov models to ascertain what’s really in dubious tinned meat products #horse #altbioinf
PhyloPithier: attempts to assign metagenomic data to taxons then makes a sarcastic remark about how badly it performed #altbioinf
BASTA : a new structured format storing infinite amount of sequences without any way to retrieve them #altbioinf
GeeGeeplot: Equestrian images R package #altbioinf
ARRR: Statistical package for pirates. #altbioinf
.@BioMickWatson MUMmYer: sequence aligner for samples of long-dead humans. #Altbioinf
and my own rather feeble contribution,
Cn3D – sensibly displays a rotating letter C #altbioinf
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
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There’s now a Storify of all of the tweets – http://storify.com/BioMickWatson/the-entire-altbioinf-stream