454 re-sequencing pipeline for bar coded samples

[david2]

Hi,

(not sure it's considered cross-posting, but as the I.SEQanswers is still in beta, I am also asking here)

I'm looking into putting together a pipeline to detect variants from bar coded samples run on a 454. Is there any consensus out there which open source tools would be useful? Or is Roche's software the current best practice?

Thanks,

David

[genehuntergirl]

Check out VIP. I have just installed it - it looks like it will do everything GSMapper does.

[sklages]

URL?

cheers,
Sven

[genehuntergirl]

http://www.ncbi.nlm.nih.gov/pubmed/20487544

For the paper. You can find in there. I don't know the URL offhand as I'm not on my work comp.

[david2]

Thanks

Thanks for the link, this looks like exactly what I need, I will try it out!

Cheers,

David

[joa_ds]

I'm glad to see people actually using the VIP pipeline.

We have been using the pipeline internally for almost a year now. But eventually, some bug will appear here and there. Please report any bug any of you might encounter, so I can fix it for a future releases.

Any questions concerning the pipeline are welcome as well.