Difference between revisions of "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 and pre-processing
 
* 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]
+
**[http://samtools.sourceforge.net/ SAMtools]
[http://picard.sourceforge.net/ Picard]
+
**[http://picard.sourceforge.net/ Picard]
[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]
+
**[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]
 
* Alignment
 
* Alignment
[http://bowtie-bio.sourceforge.net/index.shtml Bowtie]
+
**[http://bowtie-bio.sourceforge.net/index.shtml Bowtie]
[http://www.novocraft.com/main/index.php Novoalign]
+
**[http://www.novocraft.com/main/index.php Novoalign] - primarily useful for resequencing (i.e. aligning against a very similar reference genome); the free version does not support multithreading so should email and ask for a license key (supposed to be free for non-profit users)
 
* RAD
 
* RAD
 
* Gene discovery and annotation
 
* Gene discovery and annotation

Revision as of 14:18, 1 September 2011

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Welcome!

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Notes

Please add notes by topic:

  • Library prep and platform related
  • Quality Control and pre-processing
  • Assembly, de novo
  • Alignment
    • Bowtie
    • Novoalign - primarily useful for resequencing (i.e. aligning against a very similar reference genome); the free version does not support multithreading so should email and ask for a license key (supposed to be free for non-profit users)
  • RAD
  • Gene discovery and annotation
  • Variant calling
  • RNA-seq
  • Phylogenomics
  • Further analyses

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