Difference between revisions of "Nescent ngs 2011:Notebook/nescent ngs 2011"

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(Notes)
(Notes)
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**[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]
**[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 be warned, also can email and ask for a license key (1-month free for non-profit users)
 
**[http://soap.genomics.org.cn/soapaligner.html SOAPaligner/SOAP2]
 
**[http://soap.genomics.org.cn/soapaligner.html SOAPaligner/SOAP2]
 
* RAD
 
* RAD
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* Phylogenomics
 
* Phylogenomics
 
* Further analyses
 
* Further analyses
 +
* Visualization
 +
** [http://bioinf.scri.ac.uk/tablet/ Tablet] (I was trying to figure out how to look at SOAP output files and found this - SN)
  
 
==Useful Links==
 
==Useful Links==

Revision as of 12:04, 2 September 2011

<!-- sibboleth --><div id="lncal1" style="border:0px;"><div style="display:none;" id="id">lncal1</div><div style="display:none;" id="dtext"></div><div style="display:none;" id="page">Nescent ngs 2011:Notebook/nescent ngs 2011</div><div style="display:none;" id="fmt">yyyy/MM/dd</div><div style="display:none;" id="css">OWWNB</div><div style="display:none;" id="month"></div><div style="display:none;" id="year"></div><div style="display:none;" id="readonly">Y</div></div>

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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


Recent changes

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