Nescent ngs 2011:Notebook/nescent ngs 2011

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==Notes==
==Notes==
-
Please add notes by topic:
+
Please add notes by topic (note that some tools can be used in more than one analysis step):
* Library prep and platform related
* Library prep and platform related
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**[http://prinseq.sourceforge.net/ PRINSEQ]
**[http://prinseq.sourceforge.net/ PRINSEQ]
**[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://samtools.sourceforge.net/ SAMtools]
 
-
**[http://picard.sourceforge.net/ Picard]
 
-
**[http://code.google.com/p/bedtools/ bedtools]
 
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**[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]
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**[http://www.novocraft.com/main/index.php Novoalign] - primarily useful for resequencing (i.e. aligning against a very similar reference genome)
**[http://www.novocraft.com/main/index.php Novoalign] - primarily useful for resequencing (i.e. aligning against a very similar reference genome)
**[http://soap.genomics.org.cn/soapaligner.html SOAPaligner/SOAP2]  
**[http://soap.genomics.org.cn/soapaligner.html SOAPaligner/SOAP2]  
 +
**[http://sourceforge.net/apps/mediawiki/kmer/ kmer package]
* RAD
* RAD
* Gene discovery and annotation
* Gene discovery and annotation
* Variant calling
* Variant calling
 +
**[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]
* RNA-seq
* RNA-seq
* Phylogenomics
* Phylogenomics

Revision as of 19:26, 20 September 2011

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  • Here's a nice overview of a basic alignment and variant calling workflow based on SAMtools and GATK

Notes

Please add notes by topic (note that some tools can be used in more than one analysis step):

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