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

From OpenWetWare
Jump to: navigation, search
(Notes)
m (Notes)
Line 39: Line 39:
 
**[http://bowtie-bio.sourceforge.net/bowtie2 Bowtie2]
 
**[http://bowtie-bio.sourceforge.net/bowtie2 Bowtie2]
 
**[http://bio-bwa.sourceforge.net/ BWA] - Burrows-Wheeler Aligner, fast and robust
 
**[http://bio-bwa.sourceforge.net/ BWA] - Burrows-Wheeler Aligner, fast and robust
 +
**[http://research-pub.gene.com/gmap GSNAP]
 +
**[http://www.sanger.ac.uk/resources/software/smalt SMALT]
 
**[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]  
Line 44: Line 46:
 
**[http://sourceforge.net/apps/mediawiki/kmer kmer package]
 
**[http://sourceforge.net/apps/mediawiki/kmer kmer package]
 
**[http://bioinformatics.bc.edu/marthlab/Mosaik Mosaik]
 
**[http://bioinformatics.bc.edu/marthlab/Mosaik Mosaik]
**[http://research-pub.gene.com/gmap GSNAP]
 
**[http://www.sanger.ac.uk/resources/software/smalt SMALT]
 
 
*** 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
 
* Scaffolder
 
* Scaffolder

Revision as of 12:47, 11 June 2012

<!-- 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>

Owwnotebook icon.png <sitesearch>title=Search this Project</sitesearch>

Customize your entry pages <html><img src="/images/a/aa/Help.png" border="0" /></html>

Welcome!

  • Share notes and comments from the course and beyond!
  • Nescent hosted course materials are here
  • I found this page very helpful in just getting started
  • Helpful notes and tutorials from the MSU course are here
  • More from a Broad Institute workshop here
  • Some more notes
  • 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


Recently Edited Notebook Pages