| CARVIEW |
Select Language
HTTP/1.1 200 OK
Connection: keep-alive
Server: nginx/1.24.0 (Ubuntu)
Content-Type: text/html; charset=utf-8
Cache-Control: public, max-age=300
Content-Encoding: gzip
Via: 1.1 varnish, 1.1 varnish
Accept-Ranges: bytes
Age: 0
Date: Sun, 18 Jan 2026 04:49:09 GMT
X-Served-By: cache-dfw-kdal2120048-DFW, cache-bom-vanm7210049-BOM
X-Cache: MISS, MISS
X-Cache-Hits: 0, 0
X-Timer: S1768711749.823347,VS0,VE293
Vary: Accept, Accept-Encoding
transfer-encoding: chunked
simseq: Simulate sequencing with different models for priming and errors
[Skip to Readme]
simseq: Simulate sequencing with different models for priming and errors
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.
[Skip to Readme]
Downloads
- simseq-0.0.tar.gz [browse] (Cabal source package)
- Package description (as included in the package)
Maintainer's Corner
For package maintainers and hackage trustees
Candidates
- No Candidates
| Versions [RSS] | 0.0 |
|---|---|
| Dependencies | base, bio (>=0.2), bytestring, random [details] |
| License | LicenseRef-GPL |
| Author | Ketil Malde |
| Maintainer | Ketil Malde <ketil@malde.org> |
| Uploaded | by GwernBranwen at 2008-03-08T04:16:44Z |
| Category | Bioinformatics |
| Home page | https://malde.org/~ketil/ |
| Distributions | |
| Reverse Dependencies | 1 direct, 0 indirect [details] |
| Executables | simseq |
| Downloads | 1244 total (3 in the last 30 days) |
| Rating | (no votes yet) [estimated by Bayesian average] |
| Your Rating |
|
| 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. Synopsis -------- 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. Install ------- 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 malde.org>.