There is an excellent discussion of an excellent post on marginal improvements over at biomickwatson. He calls for an embargo on short read alignment tools, because there now already 70+ of them out there.
I can’t help but say – I’m sorry, but isn’t this a waste of time, both yours and mine?
I have nothing against the authors of the new tool, whom I am sure are excellent scientists. […] But still, rather than write another tool, why not contribute to the codebase of an existing tool? If BWA is not accurate enough for you, then branch the code and make it so; if Stampy is too slow, speed it up. *
That reminds me of my own rant against marginal improvements: ‘Spare me your method, show me your finding‘. What is true for aligners is true for the rest of bioinformatics too. I have seen thousands of microarray clustering, network reconstruction and enrichment analysis papers – all of them rephrasing the same small number of ideas.
You need to read the comments thread under Mick’s post. Well-argued and diverse opinions. I particularly liked this comment:
It is a false and wasteful economy to value a paper over the software it describes, but will the madness never end?