Nescent ngs 2011:Notebook/nescent ngs 2011

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m (Notes)
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**[http://picard.sourceforge.net/ Picard]
**[http://picard.sourceforge.net/ Picard]
**[http://code.google.com/p/bedtools/ bedtools]
**[http://code.google.com/p/bedtools/ bedtools]
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**[http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit GATK]
+
**[http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit GATK] (but also check out their community [http://getsatisfaction.com/gsa site])
 +
**[http://www.broadinstitute.org/software/syzygy/home Syzygy] for pooled sequencing
 +
**[http://atgu.mgh.harvard.edu/plinkseq/ PLINK/SEQ]
* RNA-seq
* RNA-seq
* Phylogenomics
* Phylogenomics

Revision as of 19:05, 1 December 2011

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Welcome!

  • Share notes and comments from the course and beyond!
  • Nescent hosted course materials are here
  • I found this page very helpful in just getting started
  • Helpful notes and tutorials from the MSU course are here
  • More from a Broad Institute workshop 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):

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