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

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**[http://www.novocraft.com/main/index.php Novoalign] - primarily useful for resequencing (i.e. aligning against a very similar reference genome)
 
**[http://www.novocraft.com/main/index.php Novoalign] - primarily useful for resequencing (i.e. aligning against a very similar reference genome)
 
**[http://soap.genomics.org.cn/soapaligner.html SOAPaligner/SOAP2]  
 
**[http://soap.genomics.org.cn/soapaligner.html SOAPaligner/SOAP2]  
 +
**[http://www.well.ox.ac.uk/project-stampy Stampy]
 
**[http://sourceforge.net/apps/mediawiki/kmer/ kmer package]
 
**[http://sourceforge.net/apps/mediawiki/kmer/ kmer package]
 
*** How do you assess/compare the quality of your assembly? Here's [http://assemblathon.org/assemblathon-1-results one way], from Assemblathon 2010
 
*** How do you assess/compare the quality of your assembly? Here's [http://assemblathon.org/assemblathon-1-results one way], from Assemblathon 2010

Revision as of 14:05, 17 October 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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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
  • 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


Recently Edited Notebook Pages