Python for genomics

[Alistair Miles]

Hi all,

I’m a research at Oxford University working on malaria genomics. Over the last couple of years, several of my colleagues and I have got a huge amount of benefit from the growing collection genomics-related software for Python. It seems like things are moving very quickly right now and there is a lot of momentum, both within the genomics domain and more broadly in general Python scientific computing. I’m very excited because I think there are great prospects for being able to do wonderful things with the ever growing scale of genomic data.

Because things are moving fast, it can be hard to stay in touch with latest developments. Also there is a lot of know-how and experience out there but it’s sometimes hard to find the right people to ask questions or learn from. I emailed Brad last week to ask if there was a Python-genomics-y mailing list already in existence, where I might post announcements about the genomics software packages I maintain and stay in touch with other new tool developments. Brad suggested that this list could be used for that purpose, and I am all for connecting with existing communities rather than creating yet another mailing list. 

I know this list has so far been focussed on bcbio-nextgen, so this would be a broadening of scope, but if it’s OK with everyone here, I’ll start to post announcements about new releases of scikit-allel [1], vcfnp [2] and pysamstats [3]. I’ll also ask my colleagues Ben Jeffery and Nick Harding to post announcements about Panoptes [4] and the cggh/biipy docker image [5]. I’d also like to get in touch with maintainers of other tools I use like pysam [6] and msprime [7] and suggest they post release announcements here. If you have any objections at all, or feel any of this is too broad or off-topic for this list, please let me know, the last thing I want to do is clog up anyone’s inbox.

Brad also suggested to try gitter as a more interactive alternative to email, so I’ve set up a gitter room at https://gitter.im/cggh/pygenomics and will also cross-post software announcements there, as well as try to be as responsive as possible. Please feel free to join and discuss anything related to the use of Python software for genomics.

Thanks,

Alistair

[1] http://scikit-allel.readthedocs.org/en/latest/

[2] https://github.com/alimanfoo/vcfnp

[3] https://github.com/alimanfoo/pysamstats

[4] https://github.com/cggh/panoptes

[5] https://github.com/cggh/biipy

[6] https://pysam.readthedocs.org/en/latest/

[7] https://msprime.readthedocs.org/en/latest/

[Daniel Gaston]

Sounds like a good idea to me. A lot of discussion on this forum has also been about the tools that are a part of the bcbio workflow, the workflows themselves, parameter choices, etc. So I think it is a pretty good fit. Just my two cents as a user.