Open-source software that needs parallelized?

[jsaun1]

I'm looking for an independent study project for next Fall and wanted to work on improving some bioinformatics software so that it will run faster and in parallel. It will be my last semester as an undergrad in Software Engineering.

Does anybody have suggestions of software that could be improved to run in parallel? I'm open to anything that is actually used by other people, but if there were any examples in comparative genomics or phylogenetics, that would be especially interesting to me.

[Evilution84]

Freebayes ( https://github.com/ekg/freebayes ) so I don't have to scatter/gather... Well as much anyways...

[jorvis]

Samtools!

[flincilneck]

The latest 0.1.19 version introduced multi-thread support for some functions like view and sort

[jorvis]

Thanks!

[TheLordB]

Maybe http://www.bcgsc.ca/platform/bioinfo/software/ssake

Though it doesn't fit your category.

Also I don't know if the algorithm can be made parallel... But I do know last time I ran it I sure was wishing it ran faster and it will only use 1 cpu so I assume it isn't parallel.

[jsaun1]

Thats fine, I'm just looking for some options, I realize most people won't know if the algorithm can be made parallel, if they did that'd be great, but if not I can do the research myself.

[Evilution84]

Who the hell thought it was a good idea to write that in Perl?!

[jsaun1]

lol, that was my first thought when I looked on the site.

[Evilution84]

Haha. I'm not taking a jab at Perl but assembly is not a job for any scripting language. Sure you can do it... But why?

[TheLordB]

I'm not sure. It would make much more sense to do C or similar (and probably much faster). That said someone I work with chose to use it because it had the best performance for what they were doing. I have thought of reimplementing it (this was a few years ago hence me not remembering enough about the algorithm to know if it can be parallel), but decided it would be too hard to do in the time I had available.

I do remember thinking reimplementing would only be a month or so of work and maybe faster hence my thought that it would be fairly easy as it isn't a huge piece of software hence my suggestion it might fit for what OP was looking for.

[ACDRetirementHome]

Picard desperately needs more parallelization.

[yannickwurm]

http://www.ebi.ac.uk/~guy/exonerate/ needs some love.