Hadoop - Revision history

Fkolpakov@gmail.com at 04:16, 17 November 2013

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 Survey of MapReduce frame operation in bioinformatics <cite>Zou2013</cite>.
 ==List of Hadoop applications for NGS==
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 #Langmead2010 pmid=20701754
 </biblio>

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	The open source Apache Hadoop project, which adopts the MapReduce framework and a distributed file system, has recently given bioinformatics researchers an opportunity to achieve scalable, efficient and reliable computing performance on Linux clusters and on cloud computing services.		The open source Apache Hadoop project, which adopts the MapReduce framework and a distributed file system, has recently given bioinformatics researchers an opportunity to achieve scalable, efficient and reliable computing performance on Linux clusters and on cloud computing services.

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 Amazon EC2
 |http://bowtie-bio.sourceforge.net/crossbow
 |-
 |BlueSNP <cite>Huang2013</cite>
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 |http://github.com/ibm-bioinformatics/bluesnp
 |}
 ==References==
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 #Nguyen2011 pmid=21645377
 #Schatz2009 pmid=19357099
 </biblio>

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 Amazon EC2, Java
 |http://sourceforge.net/projects/cloudaligner/files/
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 |cloud computing tool for identifying SNPs from high-coverage, short-read resequencing data. Two robust tools, Bowtie and SOAPsnp, implement the fundamental alignment and variant calling operations respectively, and have demonstrated capabilities within Crossbow of analyzing approximately one billion short reads per hour on a commodity Hadoop cluster with 320 cores.
 Amazon EC2
+|http://bowtie-bio.sourceforge.net/crossbow
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 |BlueSNP <cite>Huang2013</cite>
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 |http://github.com/ibm-bioinformatics/bluesnp
 |}
 ==References==
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 #Hong2012 pmid=2225766
 #Nguyen2011 pmid=21645377
 </biblio>

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 Seal is part of the Biodoop suite of tools.
 |http://biodoop-seal.sourceforge.net/
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 |http://github.com/ibm-bioinformatics/bluesnp
 |}
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 #Niemenmaa2012 pmid=22302568
 #Hong2012 pmid=2225766
 </biblio>

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 Amazon EC2, Java
 |http://transcriptome.ens.fr/eoulsan/
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 |Biodoop
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 |}
 ==References==
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 #Jourdren2012 pmid=22492314
 #Niemenmaa2012 pmid=22302568
 </biblio>

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 |http://sourceforge.net/projects/seqpig/
 http://seqpig.sourceforge.net/ (manual)
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 |BioPig <cite>#Nordberg2013</cite>
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 |http://code.google.com/p/distmap/
 http://code.google.com/p/distmap/wiki/Manual
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 It uses RHIPE R package (http://www.datadr.org) for authoring and running MapReduce programs from within the R environment.
 |http://github.com/ibm-bioinformatics/bluesnp
 |}
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 #Pandey2013 pmid=24009693
 #Huang2013 pmid=23202745
 </biblio>

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 |http://sourceforge.net/projects/seqpig/
 http://seqpig.sourceforge.net/ (manual)
 |}
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 ==References==
 <biblio>
 #Schumacher2013 pmid=24149054
 </biblio>