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Lab Software
FastQC (0.11.2)
path = /usr/local/bioinformatics/FastQC/
Trimmomatic (0.30)
path = /usr/local/bioinformatics/Trimmomatic-0.30/
Trinotate (Release 2014-07-08)
path = /usr/local/bioinformatics/Trinotate_r20140708/
bedtools (2.22.1)
path = /usr/local/bioinformatics/bedtools-2.22.1/
bismark (0.14.2)
path = /usr/local/bioinformatics/bismark_v0.14.2/
bowtie (1.0.0)
path = /usr/local/bioinformatics/bowtie-1.0.0/
bowtie2 (2.1.0)
path = /usr/local/bioinformatics/bowtie2-2.1.0/
cufflinks (2.2.1.OSX_x86_64)
path = /usr/local/bioinformatics/cufflinks-2.2.1.OSX_x86_64/
fastx_toolkit (0.0.13.2)
path = /usr/local/bioinformatics/fastx_toolkit-0.0.13.2/
hmmer (3.1b1)
path = /usr/local/bioinformatics/hmmer-3.1b1/
libgtextutils (0.6.1)
path = /usr/local/bioinformatics/libgtextutils-0.6.1/
ncbi-blast (2.2.29+)
path = /usr/local/bioinformatics/ncbi-blast-2.2.29+/
ngsplot (2.08)
path = /usr/local/bioinformatics/ngsplot-2.08/
rsem (1.2.10)
path = /usr/local/bioinformatics/rsem-1.2.10/
signalp (4.1)
path = /usr/local/bioinformatics/signalp-4.1/
stacks (1.13)
path = /usr/local/bioinformatics/stacks-1.13/
tophat (2.0.13.OSX_x86_64)
path = /usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/
trinity (Release 2013-11-10)
path = /usr/local/bioinformatics/trinityrnaseq_r20131110/
ipython (3.0.0)
Geneious (5.3.6)
FastQC (0.11.5)
path = /Users/Shared/bioinformatics/FastQC/
Trimmomatic (0.30)
path = /Users/Shared/bioinformatics/Trimmomatic-0.36/
Trinotate (3.0.1)
path = /Users/Shared/bioinformatics/Trinotate-3.0.1/
bedtools (2.26.0)
path = /Users/Shared/bioinformatics/bedtools2/
bismark (0.16.3)
path = /Users/Shared/bioinformatics/bismark_v0.15.0/
bowtie (1.1.2)
path = /Users/Shared/bioinformatics/bowtie1-1.1.2
bowtie2 (2.2.9)
path = /Users/Shared/bioinformatics/bowtie2-2.2.9
cufflinks (2.2.1.OSX_x86_64)
path = /Users/Shared/bioinformatics/cufflinks-2.2.1.OSX_x86_64
hmmer (3.1b2)
path = /Users/Shared/bioinformatics/hmmer-3.1b2-macosx-intel
ncbi-blast (2.5.0)
path = /Users/Shared/bioinformatics/ncbi-blast-2.5.0+
ngsplot (2.08)
path = /Users/Shared/bioinformatics/ngsplot
rsem (1.3.0)
path = /Users/Shared/bioinformatics/RSEM-1.3.0
stacks (1.44)
path = /Users/Shared/bioinformatics/stacks-1.44
tophat (2.1.1)
path = /Users/Shared/bioinformatics/tophat-2.1.1.OSX_x86_64
trinity (2.3.2)
path = /Users/Shared/bioinformatics/trinityrnaseq-Trinity-V2.3.2
Bismark (0.16.3)
path = /home/shared/Bismark
BSMap (2.90)
path = /home/shared/bsmap
Comet (2016.01 rev2)
path = /home/shared/comet/comet.2016012.linux.exe
FastQC (0.11.5)
path = /home/shared/fastQC/fastqc/
Pecan (?)
path = /usr/local/bin/pecan
ProteinDigestionSimulator (2.2.6318.19320)
path = /home/shared/ProtDigSim (note: This only works for the srlab user account)
ReAdW (4.3.1)
path = /home/shared/ReAdW/ReAdW.2016012.msfilereader.exe
Trim Galore (0.4.2)
path = /home/shared/trimgalore
XInteract (v5.0, part of the Trans-Proteomic Pipeline)
path = /usr/tpp_install/tpp/bin/
Microsoft Office 2016 Pro Plus
path = C:\Program Files\Microsoft Office
Protein Digest Simulator v2.2.6138.19320
path = C:\Program Files (x86)\ProteinDigestionSimulator
Proteowizard v3.0.10577
path = C:\Program Files\ProteoWizard\ProteoWizard 3.0.10577
Skyline v3.6
path =