One of the best I've seen is MethLAB. When combined with CRAC, you are guaranteed results.

Homer drinks T-Coffee with new Tophat, shiny Cufflinks, a charming Bowtie and Tuxedo on, to BLAST some MUSCLE, when stressed, he detours to MethLAB for some CRAC!! :)

BioNOT is a searchable database of negated biomedical sentences.

Can I enlist myself here with my software?

Kitten Dereplicator

The idea was given by Pierre Lindenbaum in this post: Kitten - A DNA Sequence Dereplicator & Cluster Viewer (GUI)

I liked the idea of Tuxedo (cufflinks, tophat and bowtie) in RNA Sequencing analysis. Makes one feel like a spy or something!!

The recent addition of UPARSE to Robert Edgar's U* software (UCLUST, USEARCH, UCHIME) amuses me disproportionately to how funny it actually is.

(If you're missing the joke, this deconstruction may help: UP-ARSE)

ARYANA: Aligning Reads by Yet Another Approach

You have to admire the honesty of the name!

BMC Bioinformatics | ARYANA: Aligning Reads by Yet Another Approach http://t.co/7WqfKICbtY

— Keith Bradnam 📈 (@kbradnam) September 17, 2014

SNVER MEME APE

And for the perverts:

BEDTOOLS

These aren't purely bioinformatics methods, but they require considerable bioinformatics expertise:

ChIA-PET (See also this important related supporting material)

Hi-C (With related material on how to replicate the groundbreaking but controversial Ecto-Cooler method )

A few funny bioinformatics tool names:

• SARUMAN : Semiglobal Alignment of short Reads Using CUDA and NeedleMAN-Wunsch http://bit.ly/e0tQry
• NORMA-Gene: A simple and robust method for qPCR normalization based on target gene data http://bit.ly/iS3lLC
• Sniper: improved SNP discovery by multiply mapping deep sequenced reads http://bit.ly/m5tSZw
• LinkinPath: From Sequence to Interconnected Pathway http://bit.ly/iqDepz

I keep misreading and recalling this as INSANE

NGSANE: a lightweight production informatics framework for high-throughput data analysis, Bioinformatics 2014

The CRAPome

a contaminant repository for affinity purification-mass spectrometry data.

http://www.ncbi.nlm.nih.gov/pubmed/23921808

YASARA (*Yet Another Scientific Artificial Reality Application*)

I thought this was doomed: G-nome Surfer.

https://github.com/COMBINE-lab/simpleaf which actually stands for simple alevin-fry, and not simple as f*, but it took me longer to realize than I am willing to admit.

Amber ?

The name will likely get changed at some point (I'm slowly putting together what will likely become "MethTools"), but I picked PileOMeth as a name to intentionally be somewhat funny. I like to picture Walter White when I type it...

MethPipe always makes me laugh when I see it

http://smithlabresearch.org/downloads/methpipe-manual.pdf

A decade after this thread making fun of CRAC, Nature publishes CRAQ (Clipping information for Revealing Assembly Quality)

https://www.nature.com/articles/s41467-023-42336-w

The cycle continues.

My favourite has been Project HOPE (try to google it ;) ).

Also, there are two JANEs: http://biosemantics.org/jane and http://jane.bioapps.biozentrum.uni-wuerzburg.de Although they were not published in the same journal.

FUBAR, an improved method for detecting signatures of selection implemented within HyPhy.

http://mbe.oxfordjournals.org/content/early/2013/02/18/molbev.mst030.short

Probably abit of a UK specific one (http://www.urbandictionary.com/define.php?term=baps) but;

Bayesian Analysis of Population Structure (BAPS)

But since this was often linked with Nomenclature of Territorial Units for Statistics (Nomenclature des unités territoriales statistiques aka NUTS) presenting on the subject was a pain.

I always thought Picard was a funny name. Were the authors Star Trek fans?

Someone has been giving out awards to projects with silly accronyms.

http://www.acgt.me/blog?tag=jabba

VODKA2 - Viral Opensource DVG Key Algorithm 2

VODKA2: An accurate method to detect copy-back and deletion viral genomes from next-generation sequencing data

• https://www.biorxiv.org/content/10.1101/2023.04.25.537842v1
• https://github.com/lopezlab-washu/VODKA2

Oh and who could forget MasterBayes

https://jarrod.bio.ed.ac.uk/software.html

The Oxford Nanopore data storage format went from a design called FAST5 to SLOW5 and BLOW5

• Fast nanopore sequencing data analysis with SLOW5

Even the title above feels like a parody: Fast analysis with SLOW

... the Gods must be crazy ...

I named my tool PALO. Which in Spanish mean wooden stick... and also when you feel lazy to do something in street language.

http://evolutionarygenomics.imim.es/josepl/codeigniter/index.php/pages/view/home