Nescent ngs 2011:Notebook/nescent ngs 2011

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m (Notes)
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* Assembly, de novo
* Assembly, de novo
**[http://soap.genomics.org.cn/soapdenovo.html SOAPdenovo]
**[http://soap.genomics.org.cn/soapdenovo.html SOAPdenovo]
-
* Alignment ([http://www.massgenomics.org/short-read-aligners see this helpful post])
+
* Alignment with a reference genome
**[http://bowtie-bio.sourceforge.net/index.shtml Bowtie]
**[http://bowtie-bio.sourceforge.net/index.shtml Bowtie]
**[http://bio-bwa.sourceforge.net/ BWA] - Burrows-Wheeler Aligner, fast and robust
**[http://bio-bwa.sourceforge.net/ BWA] - Burrows-Wheeler Aligner, fast and robust
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**[http://soap.genomics.org.cn/soapaligner.html SOAPaligner/SOAP2]  
**[http://soap.genomics.org.cn/soapaligner.html SOAPaligner/SOAP2]  
**[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
* RAD
* RAD
* Gene discovery and annotation
* Gene discovery and annotation

Revision as of 14:33, 15 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
  • GAGE

Notes

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

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