Biohaskell » Downloads

Updated software versions available

ketil — Tue, 20 Jul 2010 14:43:24 +0000

I’ve just uploaded new versions of various software to HackageDB. If you have cabal-install on your system, it should now be possible to do e.g. cabal install flowsim to automatically download and compile the program and its dependencies.

bio-0.4.6: A bioinformatics library

The library provides functions and data structures to work with various kinds of bioinformatics data. It has its own page here. New features include support for BLAT’s PSL format, fixes to SFF and limiting the binary dependency to <0.5 to maintain necessary laziness.

flowsim-0.2.6: A simulator for 454 pyrosequencing data

Flowsim is new on Hackage, but also has its own page. The current version is split into two parts, clonesim which simulates fragmenting of a genome, and flowsim proper, which simulates flowgrams from the sequences, and does base- and quality calling in order to output SFF files, similar to those generated from the real thing. Flowsim will be presented at ECCB’10 in Ghent at the end of September.

flower-0.3: A set of tools to work with pyrosequencing data

This is a – dare I say bouquet? of various tools for working on and with 454 data. Flower itself extracts various information from SFF files, and is documented here, but the package includes other tools as well, namely: the quite renamable flowt which attempts to remove duplicate clones, an artifact that appears to occur frequently in these data; the more appropriately named frename which relabels reads uniquely (useful if downstream software requires it), and frecover which recovers corrupted SFF files, which happened to us once, but so far hasn’t happened again.

They should all now be a cabal install away, so if you use these, please let me know how you fare, and whether you find them useful! I also try to provide Linux binaries for recent versions, and hope to provide proper Linux distribution packages (you know, .debs and .rpms) in the future. If you want to help out, there’s also the darcs repositories for biolib, flower, and flowsim.

Tools for pyrosequencing analysis

ketil — Fri, 19 Feb 2010 21:28:27 +0000

I recently did a brief presentation of the set of tools I’ve developed for analyzing pyrosequences (the Roche 454 variety). Nothing spectacular, just an overview of various ways of slicing and dicing SFF files using tools written in Haskell. For lack of a better place to put it, I’ll drop my slides below.

flowers

A (too) brief Biohaskell presentation

ketil — Tue, 15 Sep 2009 12:27:00 +0000

I was recently in Trondheim, and got an opportunity to present Haskell to an audience of bioinformaticians. Alas, it is hard to describe Haskell in all its glory to the uninitiated in forty-five minutes, and especially when I also wanted to talk a bit about the application to bioinformatics. I left in the belief that I managed to communicate some of the ideas, and submit the slides and other material here for posterity. (I’m happy to receive comments, too, just in case I’ll do a revised version of the talk later on).