Nescent ngs 2011:Notebook/nescent ngs 2011

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(Notes)
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**[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
 +
* Scaffolder
 +
**[http://www.cbcb.umd.edu/software/bambus/#intro Bambus 2]
* RAD
* RAD
 +
**[https://www.wiki.ed.ac.uk/display/RADSequencing/Home the wiki]
* Gene discovery and annotation
* Gene discovery and annotation
* Variant calling
* Variant calling

Revision as of 16:27, 19 October 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
  • 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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