flowsim: Simulate 454 pyrosequencing

[ bioinformatics, gpl, program ] [ Propose Tags ]

Provides clonesim, a clone simulator that simulates shotgun genomic clones, and flowsim, that takes the output from clonesim (or any other Fasta-formatted file) and generates simulated reads from them mimicing Roche's 454 pyrosequencing technology, writing output in 454's native SFF format. The flowgram generation is based on empirical distributions derived from real data (although analytic distributions are available too, if you prefer).

The Darcs repository is at http://malde.org/~ketil/biohaskell/flowsim.

Versions 0.2.6, 0.2.7, 0.2.8, 0.3, 0.3.3, 0.3.4, 0.3.5
Dependencies array (>=0.1), base (==4.*), biocore (>=0.3), biofasta, biosff (>=0.3), bytestring, cmdargs (>=0.5), containers, directory, MonadRandom, mtl (>=2), random [details]
License GPL-2.0-only
Author Ketil Malde
Maintainer Ketil Malde <ketil@malde.org>
Category Bioinformatics
Home page http://biohaskell.org/Applications/FlowSim
Uploaded by KetilMalde at Tue Nov 19 15:49:01 UTC 2013
Distributions NixOS:0.3.5
Executables filtersff, gelfilter, duplicator, mutator, kitsim, clonesim, hplc, flowsim
Downloads 2924 total (82 in the last 30 days)
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Status Docs not available [build log]
Last success reported on 2015-05-19 [all 8 reports]
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