Nescent ngs 2011:Notebook/nescent ngs 2011

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(Notes)
(Notes)
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* Library prep and platform related
* Library prep and platform related
-
* Quality Control
+
* Quality Control and pre-processing
[http://hannonlab.cshl.edu/fastx_toolkit/ FASTX-Toolkit]
[http://hannonlab.cshl.edu/fastx_toolkit/ FASTX-Toolkit]
[http://sourceforge.net/apps/mediawiki/kmer/ kmer package]
[http://sourceforge.net/apps/mediawiki/kmer/ kmer package]
 +
[http://samtools.sourceforge.net/ SAMtools]
* 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 21:53, 31 August 2011

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Notes

Please add notes by topic:

  • Library prep and platform related
  • Quality Control and pre-processing

FASTX-Toolkit kmer package SAMtools

  • Assembly, de novo

SOAPdenovo

  • Alignment

Bowtie Novoalign

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

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