Nescent ngs 2011:Notebook/nescent ngs 2011

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==Useful Links==
==Useful Links==
* [http://main.g2.bx.psu.edu/ Galaxy main]
* [http://main.g2.bx.psu.edu/ Galaxy main]
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* [http://prinseq.sourceforge.net/ PRINSEQ]
 
* [http://seqanswers.com/wiki/SEQanswers SEQanswers Wiki]
* [http://seqanswers.com/wiki/SEQanswers SEQanswers Wiki]
* [http://molecularevolution.org/ molecularevolution.org]
* [http://molecularevolution.org/ molecularevolution.org]

Revision as of 12:36, 9 September 2011

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Welcome!

  • Share notes and comments from the course!
  • Nescent hosted course materials are here

Notes

Please add notes by topic:

  • Library prep and platform related
  • Quality Control and pre-processing
  • Assembly, de novo
  • Alignment see this helpful post
    • Bowtie
    • BWA
    • Novoalign - primarily useful for resequencing (i.e. aligning against a very similar reference genome); the free version does not support multithreading so be warned, also can email and ask for a license key (1-month free for non-profit users)
    • SOAPaligner/SOAP2
  • RAD
  • Gene discovery and annotation
  • Variant calling
  • RNA-seq
  • Phylogenomics
  • Further analyses
  • Visualization
    • Tablet (I was trying to figure out how to look at SOAP output files and found this - SN)

Useful Links


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