Nescent ngs 2011:Notebook/nescent ngs 2011

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* Alignment [http://www.massgenomics.org/short-read-aligners see this helpful post]
* Alignment [http://www.massgenomics.org/short-read-aligners see this helpful post]
**[http://bowtie-bio.sourceforge.net/index.shtml Bowtie]
**[http://bowtie-bio.sourceforge.net/index.shtml Bowtie]
-
**[http://bio-bwa.sourceforge.net/ BWA]
+
**[http://bio-bwa.sourceforge.net/ BWA] - Burrows-Wheeler Aligner, fast and robust
**[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]  

Revision as of 18:24, 20 September 2011

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Welcome!

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  • Nescent hosted course materials are here
  • Here's a nice overview of a basic alignment and variant calling workflow based on SAMtools and GATK

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