Lab Software

###Computer: Hummingbird ####OS: OS X (10.9.5) FastQC (0.11.2)

Trimmomatic (0.30)

Trinotate (Release 2014-07-08)

bedtools (2.22.1)

bismark (0.14.2)

bowtie (1.0.0)

bowtie2 (2.1.0)

cufflinks (2.2.1.OSX_x86_64)

fastx_toolkit (0.0.13.2)

hmmer (3.1b1)

libgtextutils (0.6.1)

ncbi-blast (2.2.29+)

ngsplot (2.08)

rsem (1.2.10)

signalp (4.1)

stacks (1.13)

tophat (2.0.13.OSX_x86_64)

trinity (Release 2013-11-10)

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 (0.15.0)

 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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