simseq: Simulate sequencing with different models for priming and errors

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This is a simulator that can generate simulated sequences -- primarily EST type sequences, but quite possibly other types as well. Mail me for further information on usage etc.

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Versions [RSS] 0.0
Dependencies base, bio (>=0.2), bytestring, random [details]
License LicenseRef-GPL
Author Ketil Malde
Maintainer Ketil Malde <>
Category Bioinformatics
Home page
Uploaded by GwernBranwen at 2008-03-08T04:16:44Z
Reverse Dependencies 1 direct, 0 indirect [details]
Executables simseq
Downloads 1197 total (6 in the last 30 days)
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Status Docs not available [build log]
All reported builds failed as of 2017-01-03 [all 7 reports]

Readme for simseq-0.0

[back to package description]
Simseq - SIMulate SEQuences.  Yep, that's real creative.


Generates a bunch of sequences from a set of reference sequences.
For ESTs, NCBI's refseq transcripts are probably good choices.

The generated sequences are generated using a model that specifies
priming conditions and error generation.

Currently, this is not very refined, you can try

	simseq --model=sanger:n,d reference.fasta

Where n indicates the number of sequences to generate, starting points
drawn from a uniform distribution, and d probability of being in the 
forward direction.  Or, even more experimentally:

	simseq --model=454:n,d

Which implemets a completely unfounded and baseless model of 454/Roche
pyrosequencing.  (Okay, actually based on a paper by Marguiles et al, but
more data is definitely a requirement).

Solexa will be installed as soon as anybody says something definitive
about the error modes.

In any case, running out of sequence results in X's, indicating vector,
which I hope makes sense for Sanger, at least.


The usual Cabal routine.  Get a working GHC compiler, install
my 'bio' library, and do:

	chmod +x Setup.hs
	./Setup.hs configure
	./Setup.hs build
	sudo ./Setup.hs install

Mail me if it didn't work - <ketil at>.