Lab Software

###Computer: Hummingbird ####OS: OS X (10.9.5)

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)

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###Computer: RoadRunner/Ostrich ####OS: OS X (10.11.6)

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

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###Computer: Emu ####OS: Ubuntu 16.04

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/

###Computer: Woodpecker ####OS: Windows 7

Protein Digest Simulator

      path = 

Skyline