Nescent ngs 2011:Notebook/nescent ngs 2011

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(Notes)
(Notes)
Line 26: Line 26:
[http://sourceforge.net/apps/mediawiki/kmer/ kmer package]
[http://sourceforge.net/apps/mediawiki/kmer/ kmer package]
[http://samtools.sourceforge.net/ SAMtools]
[http://samtools.sourceforge.net/ SAMtools]
 +
[http://picard.sourceforge.net/ Picard]
 +
[http://code.google.com/p/bedtools/ bedtools]
 +
[http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit GATK]
* Assembly, de novo
* Assembly, de novo
[http://soap.genomics.org.cn/soapdenovo.html SOAPdenovo]
[http://soap.genomics.org.cn/soapdenovo.html SOAPdenovo]

Revision as of 22:12, 31 August 2011

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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

FASTX-Toolkit kmer package SAMtools Picard bedtools GATK

  • Assembly, de novo

SOAPdenovo

  • Alignment

Bowtie Novoalign

  • RAD
  • Gene discovery and annotation
  • Variant calling
  • RNA-seq
  • Phylogenomics
  • Further analyses

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