Nescent ngs 2011:Notebook/nescent ngs 2011

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(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
+
* 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://www.novocraft.com/main/index.php Novoalign] - primarily useful for resequencing (i.e. aligning against a very similar reference genome); the free version does not support multithreading so should email and ask for a license key (supposed to be free for non-profit users)
**[http://www.novocraft.com/main/index.php Novoalign] - primarily useful for resequencing (i.e. aligning against a very similar reference genome); the free version does not support multithreading so should email and ask for a license key (supposed to be free for non-profit users)
 +
**[http://soap.genomics.org.cn/soapaligner.html SOAPaligner/SOAP2]
* RAD
* RAD
* Gene discovery and annotation
* Gene discovery and annotation

Revision as of 18:31, 1 September 2011

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