View source for 1.1 RNA-Seq analysis tools

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

{| class="wikitable"
|-
! scope="col"| Tool
! scope="col"| Category
! scope="col"| URLs
|-
! scope="row"| FASTQC
|Home
| http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
|-
! scope="row"| 
|Program
| http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.6/
|-
! scope="row"|
|Manual
| http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
|-

! scope="row"| Trimmomatic
|Home
| http://www.usadellab.org/cms/?page=trimmomatic
|-
! scope="row"| 
|Program
|  http://www.usadellab.org/cms/?page=trimmomatic
|-
! scope="row"|
|Manual
| http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf
|-

! scope="row"| Bowtie2
|Home
| http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|-
! scope="row"| 
|Program
| http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.6/
|-
! scope="row"|
|Manual
|http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
|-


! scope="row"| TopHat
|Home
| https://ccb.jhu.edu/software/tophat/index.shtml
|-
! scope="row"| 
|Program
| https://ccb.jhu.edu/software/tophat/manual.shtml
|-
! scope="row"|
|Manual
|https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.0.tar.gz
|-

! scope="row"| Cufflinks
|Home
| http://cole-trapnell-lab.github.io/cufflinks/
|-
! scope="row"| 
|Program
|http://cole-trapnell-lab.github.io/cufflinks/install/
|-
! scope="row"|
|Manual
|http://cole-trapnell-lab.github.io/cufflinks/manual/
|-


! scope="row"| STAR
|Home
| https://github.com/alexdobin/STAR
|-
! scope="row"| 
|Program
|https://github.com/alexdobin/STAR/releases
|-
! scope="row"|
|Manual
|https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
|-


! scope="row"| BWA
|Home
| http://bio-bwa.sourceforge.net
|-
! scope="row"| 
|Program
|http://sourceforge.net/projects/bio-bwa/files/
|-
! scope="row"|
|Manual
|http://bio-bwa.sourceforge.net/bwa.shtml
|-


! scope="row"| Velvet
|Home
|https://www.ebi.ac.uk/~zerbino/velvet/
|-
! scope="row"| 
|Program
|https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
|-
! scope="row"|
|Manual
|https://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf
|-


! scope="row"| Samtools
|Home
|http://samtools.sourceforge.net
|-
! scope="row"| 
|Program
|http://sourceforge.net/projects/samtools/files/
|-
! scope="row"|
|Manual
|http://www.htslib.org/doc/samtools.html
|-

! scope="row"| Varscan
|Home
|http://varscan.sourceforge.net
|-
! scope="row"| 
|Program
|http://sourceforge.net/projects/varscan/files/
|-
! scope="row"|
|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