[BioC] Hello

[Martin Morgan]

On 9/25/2013 3:45 PM, jayakumar sivalingam wrote:
> Hello,
> Please let me know about the bioconductor packages to be used for the
> following things:
>
>
>     1. Quality check of the whole genome raw data
>     2. Alignment
>     3. SNP identification

In addition there is VariantTools (Linux only)

   http://bioconductor.org/packages/release/bioc/html/VariantTools.html

>     4. Annotation

   http://bioconductor.org/help/workflows/variants/

also of interest

   http://bioconductor.org/packages/release/bioc/html/AnnotationHub.html
   http://bioconductor.org/help/community/
   http://bioconductor.org/help/course-materials/2013/SeattleMay2013/

>
> Also, please let me know how I can be able to practice the above things
> with the example data and the system requirements for the same.

Many packages come with sample data sets; many vignettes and work flows are 
fully executable, look for the 'R script' on package help pages and package 
landing pages.

Packages usually operate 'across platforms' and many do not have third-party 
software requirements, although there are exceptions; actual system resources 
(e.g., memory) used vary by package and problem.

Martin

>
> Thanks & regards,
> Jai
>
> 	[[alternative HTML version deleted]]
>
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-- 
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109