Nescent ngs 2011:Notebook/nescent ngs 2011

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
m (Notes)
m (Notes)
Line 38: Line 38:
**[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 17:05, 17 October 2011

Search this Project

Customize your entry pages

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


Recent changes



Personal tools