Nescent ngs 2011:Notebook/nescent ngs 2011

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Current revision (16:47, 11 June 2012) (view source)
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**[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]  
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**[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

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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

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