Nescent ngs 2011:Notebook/nescent ngs 2011

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m (Welcome!)
m (Notes)
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**[http://prinseq.sourceforge.net/ PRINSEQ]
**[http://prinseq.sourceforge.net/ PRINSEQ]
**[http://hannonlab.cshl.edu/fastx_toolkit/ FASTX-Toolkit]
**[http://hannonlab.cshl.edu/fastx_toolkit/ FASTX-Toolkit]
 +
**[http://www.cbcb.umd.edu/software/quake/index.html Quake]
* Assembly, de novo
* Assembly, de novo
**[http://soap.genomics.org.cn/soapdenovo.html SOAPdenovo]
**[http://soap.genomics.org.cn/soapdenovo.html SOAPdenovo]

Revision as of 22:12, 11 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
  • 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

Notes

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

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