Difference between revisions of "1.1 RNA-Seq analysis tools"

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For a more complete overview of next generation sequencing software tools required for
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basic pipelines and for more advanced analysis see:
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    http://seqanswers.com/wiki/Software/list

Revision as of 21:00, 24 January 2016

The table below provides the tools for RNA-Seq analysis that you will use in this tutorial.

Tool Category URLs
FASTQC Home http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Program http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.6/
Manual http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
Trimmomatic Home http://www.usadellab.org/cms/?page=trimmomatic
Program http://www.usadellab.org/cms/?page=trimmomatic
Manual http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf
Bowtie2 Home http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Program http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.6/
Manual http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
TopHat Home https://ccb.jhu.edu/software/tophat/index.shtml
Program https://ccb.jhu.edu/software/tophat/manual.shtml
Manual https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.0.tar.gz
Cufflinks Home http://cole-trapnell-lab.github.io/cufflinks/
Program http://cole-trapnell-lab.github.io/cufflinks/install/
Manual http://cole-trapnell-lab.github.io/cufflinks/manual/
STAR Home https://github.com/alexdobin/STAR
Program https://github.com/alexdobin/STAR/releases
Manual https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
BWA Home http://bio-bwa.sourceforge.net
Program http://sourceforge.net/projects/bio-bwa/files/
Manual http://bio-bwa.sourceforge.net/bwa.shtml
Velvet Home https://www.ebi.ac.uk/~zerbino/velvet/
Program https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
Manual https://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf
Samtools Home http://samtools.sourceforge.net
Program http://sourceforge.net/projects/samtools/files/
Manual http://www.htslib.org/doc/samtools.html
Varscan Home http://varscan.sourceforge.net
Program http://sourceforge.net/projects/varscan/files/
Manual http://varscan.sourceforge.net/using-varscan.html


For a more complete overview of next generation sequencing software tools required for basic pipelines and for more advanced analysis see: 

    http://seqanswers.com/wiki/Software/list
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