101 questions with a bioinformatician #20: Roy Chaudhuri

This post is part of a series that interviews some notable bioinformaticians to get their views on various aspects of bioinformatics research. Hopefully these answers will prove useful to others in the field, especially to those who are just starting their bioinformatics careers.

Roy Chaudhuri is a Lecturer in Bioinformatics in the Department of Molecular Biology and Biotechnology at the University of Sheffield, and is part of the Sheffield Bioinformatics Hub. Roy's expertise concerns the comparative genomics and phylogenetics of bacterial pathogens and in a previous life he helped set up the coliBASE and xBASE databases. In a previous-previous life he was also a pioneering website designer (I shouldn't judge: people in glass houses… and all that).

He claims that his current duties involve "research, teaching, publishing, and trying to convince people to give me money". If you would like to give Roy money (perhaps a £1 donation towards his Eccles Cake fund?), you can get in contact with him via the Sheffield Bioinformatics Hub website. You can also find out more about Roy by following him on twitter (@RoyChaudhuri)…but be warned, he is a non-stop tweeter! And now, on to the 101 questions...

001. What's something that you enjoy about current bioinformatics research?

I like that after 16 years as a bioinformatician, I'm still learning new things every day, and that there's no shortage of cool datasets and interesting problems to keep me busy. I also like how far it's possible to get by knowing a little bit of biology and a little Perl.

010. What's something that you don't enjoy about current bioinformatics research?

I worry that too much community effort has been devoted to dealing with problems that are specific to short-read data. I'd like to think that in five years time sequencing will just work, and we will be able to devote our time to dealing with biological quirks rather than technical ones. I'm pretty sure I said the same thing five years ago, though.

011. If you could go back in time and visit yourself as a 18 year old, what single piece of advice would you give yourself to help your future bioinformatics career?

Most of my advice wouldn't be work-related, but I'd certainly mention that the clock starts ticking on potential fellowship opportunities as soon as you get your PhD. I definitely missed the starting gun on that one.

100. What's your all-time favorite piece of bioinformatics software, and why?

I'll go for Prokka, because it does an astonishingly good job at annotating bacterial genomes (better than many manual attempts...), because Torsten wrote the book (well, blog post) on creating usable command-line bioinformatics tools. I particularly like that it checks for its dependencies at the start, rather than choking half-way through, and because it sometimes finishes with a quote from the Hitchhiker's Guide to the Galaxy.

Other than that, I'm a big fan of MUMmer, and I'm always impressed by how many different things it's possible to achieve by stringing two or three SAMtools commands together. If non-bioinformatics-specific software counts, then I'd also mention GNU Parallel, Perl and UNIX itself.

101. IUPAC describes a set of 18 single-character nucleotide codes that can represent a DNA base: which one best reflects your personality, and why?

M, because it's Not K.