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 18:18, 1 September 2011

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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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