Nescent ngs 2011:Notebook/nescent ngs 2011

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
m (Notes)
(Notes)
Line 54: Line 54:
**[http://code.google.com/p/bedtools/ bedtools]
**[http://code.google.com/p/bedtools/ bedtools]
**[http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit GATK] (but also check out their community [http://getsatisfaction.com/gsa site])
**[http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit GATK] (but also check out their community [http://getsatisfaction.com/gsa site])
 +
**[http://snpeff.sourceforge.net/ snpEff]
**[http://www.broadinstitute.org/software/syzygy/home Syzygy] for pooled sequencing
**[http://www.broadinstitute.org/software/syzygy/home Syzygy] for pooled sequencing
**[http://atgu.mgh.harvard.edu/plinkseq/ PLINK/SEQ]
**[http://atgu.mgh.harvard.edu/plinkseq/ PLINK/SEQ]

Revision as of 16:20, 19 March 2012

Search this Project

Customize your entry pages

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


Recent changes



Personal tools