The Phrase That Makes Bioinformaticians Grind Their Teeth: Another Short-Read Genome Assembler

Michael Barton laments the state of bioinformatics software:

Grants are harder and harder to obtain, yet we fund the current attrition of moving bioinformatics software forward one reinvention at a time. Where else is it acceptable to reinvent a tool rather than try to improve upon an existing one? Count how many types of webservers are commonly used across the web, then count how many different genome assemblers have been published. If we were a company and we behaved this way, we would have gone out of business long ago. We have accepted a state whereby the short-term reward of publication trumps the longer-term goal of maintaining and improving existing open-source software.

Another issue Barton didn’t raise is that the improvements are pretty marginal at this point. At last count, there were 73 short-read assemblers. By the time we reached number 46, we were doing pretty well–you can only get so much blood from a stone. There’s no way anyone can keep track of them, and even someone as crazy as Nick Loman can’t test all of them.

I will now go outside and yell at clouds.

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