Software

Software installed on the clusters is available for public use without restriction.  Users must be comfortable in a Unix environment and understand how to properly submit jobs.  The Xanadu cluster is replacing the BBC cluster for research use.  Request additional information, accounts, and software installs for Xanadu here.

Software Categories:

Please note that not all installed versions are listed below. For a complete list of available software use the command: module avail
All softwares listed current as of 01/02/2019
To list all programing tools and libraries click here.

 

ChIP-Seq/Methyl-Seq Analysis

Software Version module 
Bismark 0.19.0 module load bismark/0.19.0
macs 1.4.2 module load macs/1.4.2
macs2 2.1.1.20160309 module load macs2/2.1.1.20160309
NucleoATAC 0.3.4 module load NucleoATAC/0.3.4
peakSplitter cpp_0.1 module load peakSplitter/cpp_0.1

Data Transfer

Software Version module 
BaseMount 0.13.3.1573 module load basemount/0.13.3.1573
BaseSpaceCLI 0.8.1 module load basespace-cli/0.8.1
edirect 20180312 module load edirect/20180312
GDC_Data_Transfer_Tool 1.3.0 module load GDC_Data_Transfer_Tool/1.3.0
sratoolkit 2.8.2 module load sratoolkit/2.8.2

Database

Software Version module 
postgresql 9.2.24-1 module load postgresql-client/9.2.24-1
sqlite 3.16.2 module load sqlite/3.16.2

Genome Assembly

Software Version module 
abyss 2.1.4 module load abyss/2.1.4
AlignGraph v1 module load AlignGraph/v1
AMOS 3.1.0 module load AMOS/3.1.0
CAMSA 1.0.0 module load camsa/1.0.0
Canu 1.6 module load canu/1.6
CAP3 02.10.15 module load CAP3/02.10.15
DISCOVAR de novo 52488 module load DiscovarDeNovo/52488
flye 2.3.7 module load flye/2.3.7
GapFiller 2.1.1 module load GapFiller/2.1.1
GMcloser 1.6.2 module load GMcloser/1.6.2
Jellyfish 2.2.6 module load jellyfish/2.2.6
MaSuRCA 3.2.6 module load MaSuRCA/3.2.6
Metassembler 1.5 module load Metassembler/1.5
nanocorrect 2015 module load nanocorrect/2015
nanopolish 0.10.2 module load nanopolish/0.10.2
pandaseq 2.11 module load pandaseq/2.11
Phrap 1.090518 module load phrap/1.090518
pilon 1.22 module load pilon/1.22
Platanus 1.2.4 module load Platanus/1.2.4
platanus-allee 2.0.1 module load platanus-allee/2.0.1
quast 5.0.2 module load quast/5.0.2
racon 0.5.0 module load racon/0.5.0
Ray 2.3.1 module load Ray/2.3.1
SOAP-denovo 2.04 module load SOAP-denovo/2.04
SPAdes 3.11.1 module load SPAdes/3.11.1
SSPACE-LongRead 1-1 module load SSPACE-LongRead/1-1
SSPACE-Standard 3.0 module load SSPACE/3.0
unicycler 0.4.3 module load unicycler/0.4.3
velvet 1.2.10_kmer151 module load velvet/1.2.10_kmer151
Phred 0.071220.c module load phred/0.071220.c

Genome Wide Methods

Software Version module 
HiC-Pro 2.10.0 module load HiC-Pro/2.10.0
ISseeker 1.1 module load ISseeker/1.1
juicer 1.8.9 module load juicer/1.8.9
w4cseq 0.1.0 module load w4cseq/0.1.0

Metagenomics

Software Version module 
bracken 1.0.0 module load bracken/1.0.0
CONCOCT 0.4.1 module load CONCOCT/0.4.1
FragGeneScan 1.30 module load FragGeneScan/1.30
HUMAnN2 0.11.1 module load humann2/0.11.1
Kraken 1.0 module load kraken/1.0
mash 2.0 module load mash/2.0
MaxBin 2.2.5 module load MaxBin/2.2.5
megahit 1.1.2 module load megahit/1.1.2
MetaBAT 2.12.1 module load metabat/2.12.1
MetaCRAST 2017 module load MetaCRAST/2017
MetaVelvet 1.2.02 module load MetaVelvet/1.2.02
microbiomeutil r20110519 module load microbiomeutil/r20110519
MinCED 0.2.0 module load MinCED/0.2.0
mothur 1.41.1 module load mothur/1.41.1
qiime 2-2018.8 module load qiime/2-2018.8
SortMeRNA 2.1b module load sortmerna/2.1b

Phylogenetics

Software Version module 
CAFÉ 4.1 module load CAFE/4.1
CheckM 1.0.7 module load CheckM/1.0.7
clearcut 1.0.9 module load clearcut/1.0.9
FastME 2.1.5 module load FastME/2.1.5
FastTree 2.1.10 module load fasttree/2.1.10
GARLI 2.01 module load garli/2.01
HyPhy 2.3.11 module load hyphy/2.3.11
IQ-TREE 1.6.6 module load iqtree/1.6.6
mashtree 0.32 module load mashtree/0.32
mauve 2015-02-13 module load mauve/2015-02-13
MetaPhlAn 2.0 module load MetaPhlAn/2.0
Migrate-n 3.6.11 module load migrate/3.6.11
MrBayes 3.2.7 module load MrBayes/3.2.7
OrthoFinder 2.1.2 module load OrthoFinder/2.1.2
PAML 4.9 module load paml/4.9
PAUP* 4.0a-163 module load paup/4.0a-163
phylip 3.697 module load phylip/3.697
PhyloSift 1.0 module load PhyloSift/1.0
PhyML 3.1 module load PhyML/3.1
pplacer 1.1a19 module load pplacer/1.1a19
RAxML 8.2.11 module load RAxML/8.2.11
scythe 0.991 module load scythe/0.991
tree-puzzle 5.3.rc16 module load tree-puzzle/5.3.rc16
treeFix-DTL 1.0.2 module load treefixDTL/1.0.2

Population Genetics

Software Version module 
arlecore 3.5.2.2 module load arlecore/3.5.2.2
arlsumstat 3.5.2.2 module load arlsumstat/3.5.2.2
BAPS 6.0 module load BAPS/6.0
BayesAss 3.0.4 module load BayesAss/3.0.4
BOLT-LMM 2.2 module load bolt/2.2
fastStructure 1.0 module load fastStructure/1.0
qctool 2.0-rc9 module load qctool/2.0-rc9
RefineM 0.0.20 module load refinem/0.0.20
structure 2.3.4 module load structure/2.3.4

Proteomics

Software Version module 
omssa 2.1.9 module load omssa/2.1.9
PeptideShaker 1.14.6 module load PeptideShaker/1.14.6

RAD-Seq

Software Version module 
dDocent 2.2.16 module load dDocent/2.2.16
ipyrad 0.7.22 module load ipyrad/0.7.22
pyrad 3.0.66 module load pyrad/3.0.66
rainbow 2.0.4 module load rainbow/2.0.4
stacks 2.2 module load stacks/2.2

Repeat Identification

Software Version module 
CRISPRDetect 2.2 module load CRISPRDetect/2.2
RECON 1.08v module load RECON/1.08v
RepeatMasker 4.0.6 module load RepeatMasker/4.0.6
RepeatModeler 1.0.8 module load RepeatModeler/1.0.8
RepeatScout 1.0.5 module load RepeatScout/1.0.5
rmblastn 2.6.0 module load rmblastn/2.6.0
Sputnik sputnik-monomucleotide module load sputnik/sputnik-monomucleotide
TRF 4.09 module load TRF/4.09

RNA Structure

Software Version module 
LocARNA 1.8.10 module load locarna/1.8.10
RNAz 2.1 module load RNAz/2.1
reapr 1.0.18 module load reapr/1.0.18

Sequence Alignment/Annotation

Software Version module 
antiSMASH 3.0 module load antiSMASH/3.0
aragorn 1.2.38 module load aragorn/1.2.38
Augustus 3.2.3 module load augustus/3.2.3
bamtools 2.5.1 module load bamtools/2.5.1
BARRNAP 0.6 module load barrnap/0.6
bedtools 2.27.1 module load bedtools/2.27.1
BEDtools 2.27.1 module load BEDtools/2.27.1
blast 2.7.1 module load blast/2.7.1
Blat 36×2 module load Blat/36×2
BRAKER 2.1.0 module load BRAKER/2.1.0
busco 3.0.2b module load busco/3.0.2b
CD-HIT 4.6.8 module load cdhit/4.6.8
clustalw 2.1 module load clustalw/2.1
DIAMOND 0.9.19 module load diamond/0.9.19
eggnog-mapper 0.99.1 module load eggnog-mapper/0.99.1
ELPH 2005 module load elph/2005
emboss 6.6.0 module load emboss/6.6.0
EVidenceModeler 1.1.1 module load EVidenceModeler/1.1.1
Exonerate 2.4.0 module load exonerate/2.4.0
fastmiso e0f52c0 module load fastmiso/e0f52c0
gemma 0.97 module load gemma/0.97
genomethreader 1.7.1 module load genomethreader/1.7.1
GenomeTools 1.5.10 module load genometools/1.5.10
GET_HOMOLOGUES 3.1.0 module load get_homologues/3.1.0
gffcompare 0.10.4 module load gffcompare/0.10.4
gffread 0.9.12 module load gffread/0.9.12
glimmerhmm 3.0.4 module load glimmerhmm/3.0.4
gridss 1.5.1 module load gridss/1.5.1
HMMER 3.2.1 module load hmmer/3.2.1
Infernal 1.1.1 module load infernal/1.1.1
InterProScan 5.25-64.0 module load interproscan/5.25-64.0
last 475 module load last/475
legacy-blast 2.2.22 module load legacy-blast/2.2.22
MAFFT 7.305 module load mafft/7.305
MAKER 2.31.9 module load maker/2.31.9
meme 4.11.2_2 module load meme/4.11.2_2
minimap2 20170804 module load minimap2/20170804
miso 0.5.4 module load miso/0.5.4
MISO 0.5.3 module load MISO/0.5.3
MUMmer 4.0.2 module load MUMmer/4.0.2
MUSCLE 3.8.31 module load muscle/3.8.31
PASApipeline 2.3.3 module load PASApipeline/2.3.3
PBSuite 15.8.24 module load PBSuite/15.8.24
pear 0.9.11 module load pear/0.9.11
PrAS beta module load PrAS/beta
prodigal 2.6.3 module load prodigal/2.6.3
prokka 1.11 module load prokka/1.11
seaview 4.7 module load seaview/4.7
seqtools 4.42.1 module load seqtools/4.42.1
signalp 4.1 module load signalp/4.1
snap 2013-11-29 module load snap/2013-11-29
SNP2HLA 1.0.3 module load SNP2HLA/1.0.3
spaln 2.3.1 module load spaln/2.3.1
subread 1.6.0 module load subread/1.6.0
taco 0.7.3 module load taco/0.7.3
uclust 1.2.22q module load uclust/1.2.22q
ucsc_genome 2012.05.22 module load ucsc_genome/2012.05.22
usearch 9.0.2132 module load usearch/9.0.2132
vsearch 2.4.3 module load vsearch/2.4.3
yaha 0.1.83 module load yaha/0.1.83
Glimmer 3.02 module load glimmer/3.02

Short Read Alignment and Quality Control

Software Version module 
AfterQC 0.9.6 module load AfterQC/0.9.6
AmpliconNoise 1.29 module load AmpliconNoise/1.29
autobarcode 2.1.2 module load autobarcode/2.1.2
bamutil 1.0.7 module load bamutil/1.0.7
BBMap 37.41 module load bbmap/37.41
bcl2fastq 2.20 module load bcl2fastq/2.20
BFAST 0.7.0a module load bfast/0.7.0a
bowtie 1.1.2 module load bowtie/1.1.2
bowtie2 2.3.3.1 module load bowtie2/2.3.3.1
BWA 0.7.17 module load bwa/0.7.17
cdbtools 0.99 module load cdbtools/0.99
FastQC 0.11.7 module load fastqc/0.11.7
FASTX-Toolkit 0.0.13 module load fastx/0.0.13
flexbar 3.4 module load flexbar/3.4
GMAP 2017-03-17 module load gmap/2017-03-17
graphmap 0.5.1 module load graphmap/0.5.1
HISAT2 2.1.0 module load hisat2/2.1.0
htseq 0.11.0 module load htseq/0.11.0
mirdeep2 2.0.0.8 module load mirdeep2/2.0.0.8
MultiQC 1.6 module load MultiQC/1.6
NxTrim 0.4.1 module load NxTrim/0.4.1
picard 2.9.2 module load picard/2.9.2
poretools 0.6.0 module load poretools/0.6.0
pysam 0.11.2.2 module load pysam/0.11.2.2
qualimap 2.2.1 module load qualimap/2.2.1
samblaster 0.1.24 module load samblaster/0.1.24
samtools 1.7 module load samtools/1.7
seqtk 1.2 module load seqtk/1.2
sickle 1.33 module load sickle/1.33
tabix 0.2.6 module load tabix/0.2.6
tbl2asn 25.6 module load tbl2asn/25.6
Trimmomatic 0.36 module load Trimmomatic/0.36
java -jar $Trimmomatic
XSQ_Tools 1.0 module load XSQ_Tools/1.0
cutadapt 1.14 module load cutadapt/1.14
deepTools 2.0 module load deeptools/2.0
DLCpar 1.0 module load DLCpar/1.0
DWGSIM 0.1.11 module load DWGSIM/0.1.11
ea-utils 1.04.807 module load ea-utils/1.04.807
CompareM 0.0.23 module load CompareM/0.0.23

Statistics

Software Version module 
R 3.5.1 module load R/3.5.1
R 3.5.2 module load R/3.5.2
Bioconductor 3.8, IRanges, GenomicRanges, DESeq2, dplyr, gplots, ggplot2, RColorBrewer, genefilter

Structure Calculations and Modeling

Software Version module 
Gaussian 16.A.03 module load gaussian/16.A.03
Gromacs 2016.1 module load Gromacs/2016.1
QuantumEspresso qe-6.1 module load QuantumEspresso/qe-6.1
randfold 2.0.1 module load randfold/2.0.1
ViennaRNA 2.2.7 module load ViennaRNA/2.2.7
vina 1.1.2 module load vina/1.1.2

Transcriptomics

Software Version module 
bcftools 1.6 module load bcftools/1.6
Cell Ranger 2.1.1 module load cellranger/2.1.1
Cufflinks 2.2.1 module load cufflinks/2.2.1
DETONATE 1.11 module load detonate/1.11
EDGE-pro 1.3.1 module load EDGE_pro/1.3.1
EnTAP 0.8.0-beta module load EnTAP/0.8.0-beta
eXpress 1.5.1 module load express/1.5.1
FrameDP 1.2.2 module load FrameDP/1.2.2
GeneMark-ET 4.38 module load GeneMark-ET/4.38
gfold 1.1.4 module load gfold/1.1.4
HTSeq 0.9.1 module load htseq/0.9.1
idba 1.1.3 module load idba/1.1.3
isoem2 2.0.0 module load isoem2/2.0.0
jsplice 1.0.3 module load jsplice/1.0.3
Kallisto 0.44.0 module load kallisto/0.44.0
KisSplice 2.4.0-p1 module load kissplice/2.4.0-p1
mats 3.0.8 module load mats/3.0.8
miARma 1.7.1 module load miARma/1.7.1
mira 4.0.2 module load mira/4.0.2
rail-rna 0.2.4b module load rail-rna/0.2.4b
REDItools 1.0.3 module load reditools/1.0.3
rMATS 4.0.1 module load rMATS/4.0.1
rsem 1.3.0 module load rsem/1.3.0
salmon 0.9.1 module load salmon/0.9.1
STAR 2.5.3a module load STAR/2.5.3a
stringtie 1.3.4.d module load stringtie/1.3.4.d
suppa 1.0 module load suppa/1.0
tophat 2.1.1 module load tophat/2.1.1
Trans-ABySS 2.0.1 module load transabyss/2.0.1
TransDecoder 5.3.0 module load TransDecoder/5.3.0
transrate 1.0.3 module load transrate/1.0.3
Trinity 2.6.6 module load trinity/2.6.6
Trinotate 3.1.1 module load Trinotate/3.1.1

Variant Detection

Software Version module 
CASAVA 1.8.2 module load casava/1.8.2
DISCOVAR 52488 module load Discovar/52488
EXCAVATOR2 1.1.2 module load EXCAVATOR2/1.1.2
FreeBayes 1.1.0 module load freebayes/1.1.0
GATK 4.0 module load GATK/4.0
hap.py 0.3.9 module load hap.py/0.3.9
IMPUTE2 2.3.2 module load impute2/2.3.2
Long Ranger 2.2.2 module load longranger/2.2.2
marginAlign v0.1 module load marginAlign/v0.1
MuTect 1.1.4 module load MuTect/1.1.4
pindel 0.2.5b9 module load pindel/0.2.5b9
plink 1.90.beta.4.4 module load plink/1.90.beta.4.4
pyvcf 0.6.8 module load pyvcf/0.6.8
rtg-tools 3.8.4 module load rtg-tools/3.8.4
snpEff 4.3q module load snpEff/4.3q
SNPGenie 1.0 module load SNPGenie/1.0
snptest 2.5.2 module load snptest/2.5.2
varscan 2.4.3 module load varscan/2.4.3
vcflib 1.0.0-rc1 module load vcflib/1.0.0-rc1
vcftools 0.1.16 module load vcftools/0.1.16

Visualization

Software Version module 
circos 0.69-6 module load circos/0.69-6
consed 29.0 module load consed/29.0
FreeSurfer 6.0.0 module load FreeSurfer/6.0.0
FSL 5.0.10 module load FSL/5.0.10
GenomeBrowser 20180626 module load GenomeBrowser/20180626
imageMagick 6.8.9 module load imageMagick/6.8.9
ITK-SNAP 3.6.0 module load ITK-SNAP/3.6.0
majiq 0.9 module load majiq/0.9