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