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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 (

 path = /usr/local/bioinformatics/fastx_toolkit-

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

Int. HDD 1 Capacity (//home/shared/8TB_HDD_01): 8.0TB

Int. HDD 2 Capacity (/home/shared/8TB_HDD_02): 8.0TB

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

RStudio Server

  1. Activate Husky OnNet VPN service.

  2. Paste the following URL in your internet browser:


    • If you receive a notice from your browser regarding "insecure connection", you may safely ignore this and proceed.

  3. Use login credentials provided by Steven or Sam.

  4. If you encounter any issues, please create a new Issue. Please post screenshots and paste text of any error messages you encounter.

Computer: roadrunner

OS: Ubuntu 16.04

CPU(s): 16

Memory: 48GB

HDD Capacity: 1.8TB

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-  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-  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-        samtools-1.8

R (Microsoft Open R 3.5.1)
jupyter (with R Kernel)

JBrowse Genome Viewer v1.15.4

Computer: Mox (Hyak)

OS: Red Hat Enterprise 7.2 (login nodes)

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

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     Trimmomatic-0.36
bedtools-2.27.1           decorator-4.0.11  interproscan-5.31-70.0  ncbi-blast-2.6.0+            pyfaidx-         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-  gcc       maker-2.31.10       PBSuite                  RNAMMER-1.2             SSPACE-LongRead_v1-1
bsmap-2.89      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