Difference between revisions of "Hadoop"

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|http://sourceforge.net/projects/seqpig/
 
|http://sourceforge.net/projects/seqpig/
 
http://seqpig.sourceforge.net/ (manual)
 
http://seqpig.sourceforge.net/ (manual)
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|-
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|Hadoop-BAM <cite>Niemenmaa2012</cite>
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|Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools.
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The file formats currently supported are BAM, SAM, FASTQ, FASTA, QSEQ, BCF, and VCF.
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SeqPig project provides a higher-level interface to the file formats supported by Hadoop-BAM
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|http://sourceforge.net/projects/hadoop-bam/
 
|-
 
|-
 
|BioPig <cite>#Nordberg2013</cite>
 
|BioPig <cite>#Nordberg2013</cite>
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|http://code.google.com/p/distmap/
 
|http://code.google.com/p/distmap/
 
http://code.google.com/p/distmap/wiki/Manual
 
http://code.google.com/p/distmap/wiki/Manual
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|-
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|Eoulsan <cite>Jourdren2012</cite>
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|Eoulsan provides an integrated and flexible solution for RNA-Seq data analysis of differential expression.
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Amazon EC2, Java
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|http://transcriptome.ens.fr/eoulsan/
 
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|-
 
|
 
|
 
|
 
|
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|
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|-
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|Crossbow <cite>Gurtowski2012</cite>
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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.
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Amazon EC2
 
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It uses RHIPE R package (http://www.datadr.org) for authoring and running MapReduce programs from within the R environment.
 
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
 
|http://github.com/ibm-bioinformatics/bluesnp
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#Pandey2013 pmid=24009693
 
#Pandey2013 pmid=24009693
 
#Huang2013 pmid=23202745
 
#Huang2013 pmid=23202745
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#Gurtowski2012 pmid=22948728
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#Jourdren2012 pmid=22492314
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#Niemenmaa2012 pmid=22302568
 
</biblio>
 
</biblio>

Revision as of 01:19, 17 November 2013

This page or section is a stub. Please add more information here!

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.

Survey of MapReduce frame operation in bioinformatics [1].


List of Hadoop applications for NGS

Hadoop MapReduce-based approaches have become increasingly popular due to their scalability in processing large sequencing data sets[2].

Tool, Ref Description URL
SeqPig [2] A library and a collection of tools to manipulate, analyze and query sequencing data sets in a scalable and simple manner.

SeqPig scripts use the Hadoop-based distributed scripting engine Apache Pig, which automatically parallelizes and distributes data processing tasks.

http://sourceforge.net/projects/seqpig/

http://seqpig.sourceforge.net/ (manual)

Hadoop-BAM [3] Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools.

The file formats currently supported are BAM, SAM, FASTQ, FASTA, QSEQ, BCF, and VCF. SeqPig project provides a higher-level interface to the file formats supported by Hadoop-BAM

http://sourceforge.net/projects/hadoop-bam/
BioPig [4] BioPig is based on the Apache's Hadoop MapReduce system and the Pig data flow language. https://sites.google.com/a/lbl.gov/biopig/
DistMap [5] A modular, scalable and integrated workflow to map reads in the Hadoop distributed computing framework.

It accepts reads in FASTQ format as input and provides mapped reads in a SAM/BAM format. DistMap supports both paired-end and single-end reads thereby allowing the mapping of read data produced by different sequencing platforms.

Currently, DistMap supports 9 mappers:

http://code.google.com/p/distmap/

http://code.google.com/p/distmap/wiki/Manual

Eoulsan [6] Eoulsan provides an integrated and flexible solution for RNA-Seq data analysis of differential expression.

Amazon EC2, Java

http://transcriptome.ens.fr/eoulsan/
Crossbow [7] 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

BlueSNP [8] R package which distributes GWAS computation over a cluster configured with the Hadoop framework, making computationally intensive analyses, such as estimating empirical p-values via data permutation, and searching for expression quantitative trait loci over thousands of genes, feasible for large genotype-phenotype datasets.

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



References

Error fetching PMID 23396756:
Error fetching PMID 24149054:
Error fetching PMID 24021384:
Error fetching PMID 24009693:
Error fetching PMID 23202745:
Error fetching PMID 22948728:
Error fetching PMID 22492314:
Error fetching PMID 22302568:
  1. Error fetching PMID 23396756: [Zou2013]
  2. Error fetching PMID 24149054: [Schumacher2013]
  3. Error fetching PMID 22302568: [Niemenmaa2012]
  4. Error fetching PMID 24021384: [Nordberg2013]
  5. Error fetching PMID 24009693: [Pandey2013]
  6. Error fetching PMID 22492314: [Jourdren2012]
  7. Error fetching PMID 22948728: [Gurtowski2012]
  8. Error fetching PMID 23202745: [Huang2013]
All Medline abstracts: PubMed | HubMed
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