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

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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]
**[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 15:05, 1 December 2011

<!-- sibboleth --><div id="lncal1" style="border:0px;"><div style="display:none;" id="id">lncal1</div><div style="display:none;" id="dtext"></div><div style="display:none;" id="page">Nescent ngs 2011:Notebook/nescent ngs 2011</div><div style="display:none;" id="fmt">yyyy/MM/dd</div><div style="display:none;" id="css">OWWNB</div><div style="display:none;" id="month"></div><div style="display:none;" id="year"></div><div style="display:none;" id="readonly">Y</div></div>

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Customize your entry pages <html><img src="/images/a/aa/Help.png" border="0" /></html>


  • 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


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

Useful Links

Recently Edited Notebook Pages