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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)


Computer: ostrich

OS: OS X (10.11.6)

Anaconda3 (with R kernel and rpy2 for jupyter)

 path = /Users/Shared/anaconda3

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

celera assembler (8.3rc2)

path = /Users/Shared/bioinformatics/wgs-8.3rc2

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

Computer: raven

OS: Ubuntu 16.04

CPU(s): 48

Memory: 256GB

HDD Capacity: 1.0TB

Ext. HDD 1 Capacity (/media/ext_HDD01): 1.0TB

Ext. HDD 2 Capacity (/media/ext_HDD01): 1.0TB

$/home/shared
blast_dbs  blobtoolkit-v2.6.2  bowtie2-2.4.4-linux-x86_64  jellyfish-2.3.0  kallisto  ncbi-blast-2.11.0+  salmon-1.4.0_linux_x86_64  samtools-1.12  trinityrnaseq-v2.12.0

Computer: roadrunner

OS: Ubuntu 16.04

CPU(s): 16

Memory: 48GB

HDD Capacity: 1.8TB

$/home/shared
alpaca           Bismark-v0.17.0               bwa-0.7.17      igv-webapp              macau                  ncbi-blast-2.7.1+-src  RepeatMasker-4.0.7         SOAPdenovo2-r241
anaconda3        BisSNP                        ectools-0.1     jellyfish-2.2.6         meraculous-2.2.5       parallel-20180422      rmblast_2.6.0              TrimGalore-0.4.5
bbmap_38.44      bowtie2-2.3.3.1-linux-x86_64  EMBOSS-6.6.0    kallisto_linux-v0.43.1  Meraculous-v2.2.5      PBSuite_15.8.24        salmon-1.2.1_linux_x86_64  wgs-assembler
bedtools-2.28.0  bowtie2-2.3.4.1-linux-x86_64  fastqc_v0.11.7  kmergenie-1.7044        MultiQC                pecan                  samtools-1.6
bin              BSMap                         IGVTools        Log-Log4perl-1.49       ncbi-blast-2.6.0+-src  pyfaidx-0.5.3.1        samtools-1.8

/usr/bin
cutadapt
R (Microsoft Open R 3.5.1)
/home/shared/anaconda3/bin
jupyter (with R Kernel)

JBrowse Genome Viewer v1.15.4

http://roadrunner.fish.washington.edu/jbrowse/


Computer: Mox (Hyak)

OS: Red Hat Enterprise 7.2 (login nodes)

OS: CentOS Linux 7.2.1511 (build, interactive nodes, & execute nodes)

$/gscratch/srlab/programs
2bRAD_GATK            busco-v3      git-sym         mdust                    perl                samtools-1.4              supernova-2.0.0
argparse-1.4.0            bwa-0.7.15    graphviz-2.40.1     megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin  picard_2.18.4           samtools-1.9              tmhmm-2.0c
Augustus-3.3.2            bwa-0.7.17    hisat2-2.1.0        MetaGeneMark_linux_64_3.38       picard-2.9.1            scripts                   transdecoder
bamtools-2.5.1            canu      hmmer-2.3       Metassembler                 pigz-2.4            seqtk-1.3                 TransDecoder-v5.3.0
bbmap_38.34           celera        hmmer-3.1b2     minimap                  pilon               setuptools-36.0.1             TransDecoder-v5.5.0
bcftools-1.9              cmake-3.12.1  hmmer-3.2.1     mummer                   pitchfork           signalp-4.1               TrimGalore-0.4.5
bcl2fastq-v2.20           cutadapt-1.16 htslib-1.9      MUMmer3.23               platanus_1.2.4          smrtanalysis_2.3.0.140936.run     Trimmomatic-0.36
bedtools-2.27.1           decorator-4.0.11  interproscan-5.31-70.0  ncbi-blast-2.6.0+            pyfaidx-0.5.5.2         snap                  Trinity-v2.8.3
bin               FastaIndex    jellyfish-2.2.10    ncbi-blast-2.8.1+            pyScaf              SOAPdenovo2               Trinotate-v3.1.1
Bismark-0.19.0            FastQC-0.11.5 jsoncpp-1.8.4       ncbi-blast-2.8.1+_orginal        quast-4.5           SOAPec_bin_v2.03              wtdbg-2.1_x64-linux
Bismark-0.21.0            gapcloser-1.12    kmergenie-1.7048    networkx-1.11                racon               SPAdes-3.13.0-Linux
Bismark-0.21.0_dev        GARM_v0.7.5   last-852        networkx2                redundans           SparseAssembler
bowtie2-2.1.0             GATK      likelybin-0.1.0     parallel-20180822            resources           sqlite
bowtie2-2.3.4.1-linux-x86_64  gcc       maker-2.31.10       PBSuite                  RNAMMER-1.2             SSPACE-LongRead_v1-1
bsmap-2.89            get-pip.py    MaSuRCA-3.2.3       pecan                    salmon-0.11.2-linux_x86_64  SSPACE-STANDARD-3.0_linux-x86_64

Computer: woodpecker

OS: Windows 7 Enterprise (64-bit)

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 =

Computer: swan

OS: Windows 7 Enterprise (64-bit)

Microsoft Office Professional 2016 64-bit - Access - Excel - Power Point - Word

R v3.4.2

R Studio 1.1383

Skyline v3.7.0.11317

Skyline Daily v3.7.1.11446

Virtual Clonedrive v5.5.0.0

ProteoWizard 3.0.11516 64-bit - MSConvert - SeeMS

LabX v. 8.0.0 Build 3444

Protein Digest Simulator v2.2.6471; September 19, 2017