"Surely now we can have an embargo on the development and publication of short-read mappers?" he asks. "We have enough. In fact, we had enough when there were 20, never mind 70+. Do yourself, and everyone else, a favor. Stop. If you're short of things to do, why not try writing something that can align/assemble 10 [kb to] 100 kb reads instead?"
Watson acknowledges that the reason behind the proliferation of these algorithms is that "there is no incentive when one contributes to an existing, already published, codebase. As an academic, publish or perish, and if you write a new tool you will get a paper out of it; if you contribute to an existing tool, at best your name will be lost in a long list of authors, and at worst you won't get published at all."
He argues that this excuse is a "complete fallacy," however, noting that Velvet, one of the first short-read assemblers, has spawned a multitude of papers from bioinformaticians who have written wrappers or extended the code.
"Any bioinformatics codebase can be seen as a great coral reef, for many others to feed off, and to create an entire ecosystem of tools and extensions," he says. "Surely it's better that way, rather than swim off on your own and try and establish another, virtually identical reef a few miles away?"
Many commenters on the post agree with Watson that there are too many algorithms available for short read alignment, but the consensus seems to be that the pressure to publish new work is too strong for the bioinformatics community to change its habits any time soon.