[Bioc-sig-seq] Illumina CIF format for ShortRead?

Michael Muratet mmuratet at hudsonalpha.org
Thu Sep 10 20:32:44 CEST 2009


I would like to be able to use the ShortRead package on CIF file data  
from the latest version of the Illumina SCS/Pipeline tools. It appears  
that the current version of ShortRead (1.2.1?) doesn't handle this  
format. I have a snippet of a R script that will read these binary  
files and produce the same output as the Illumina cifToTxt tool and  
I'm willing to do the work to incorporate it into ShortRead. Are there  
already plans to do this? Can anyone point me to document that  
describes the basic syntax and data structures behind R objects of  
this class? I've looked at the ShortRead source and I'm not sure I  
could figure it out just from that.

Hopefully, the CIF format will be around for awhile.



Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
(256) 327-0473 (p)
(256) 327-0966 (f)

Room 4005
601 Genome Way
Huntsville, Alabama 35806

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