Difference between revisions of "Nescent ngs 2011:Notebook/nescent ngs 2011"

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* Nescent hosted course materials are [https://www.nescent.org/sites/academy/NGS_2011_Course_Materials here]
 
* Nescent hosted course materials are [https://www.nescent.org/sites/academy/NGS_2011_Course_Materials here]
 
* Helpful notes and tutorials from the MSU course are [http://ged.msu.edu/angus/index.html here]
 
* Helpful notes and tutorials from the MSU course are [http://ged.msu.edu/angus/index.html here]
* Some more [[http://molecularevolution.org/ notes]
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* Some more [http://molecularevolution.org/ notes]
 
* [http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_protocol Here]'s a nice overview of a basic alignment and variant calling workflow based on SAMtools and GATK
 
* [http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_protocol Here]'s a nice overview of a basic alignment and variant calling workflow based on SAMtools and GATK
 
* A more in-depth variant detection [http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3 strategy] based on GATK
 
* A more in-depth variant detection [http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3 strategy] based on GATK

Revision as of 12:20, 19 October 2011

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Welcome!

  • Share notes and comments from the course and beyond!
  • Nescent hosted course materials are here
  • Helpful notes and tutorials from the MSU course are here
  • Some more notes
  • Here's a nice overview of a basic alignment and variant calling workflow based on SAMtools and GATK
  • A more in-depth variant detection strategy based on GATK
  • GAGE

Notes

Please add notes by topic (note that some tools can be used in more than one analysis step):

Useful Links


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