Software

Software installed on the Xanadu cluster is available for public use without restriction.  Users must be comfortable in a Unix environment and understand how to properly submit jobs.

This list is updated infrequently. For a list of the latest software/versions please log in to the Xanadu cluster and type “module avail” at the terminal prompt.

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

To list all programing tools and libraries click here.

Also for some software we do have example scripts in our git hub page

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 2.1.2 module load macs2/2.1.2
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
gdrive 2.1.0 module load gdrive/2.1.0
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 1.8 module load canu/1.8
CAP3 02.10.15 module load CAP3/02.10.15
DISCOVAR de novo 52488 module load DiscovarDeNovo/52488
flye 2.4.2 module load flye/2.4.2
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 3.3.3 module load MaSuRCA/3.3.3
Metassembler 1.5 module load Metassembler/1.5
nanocorrect 2015 module load nanocorrect/2015
nanopolish 0.11.1 module load nanopolish/0.11.1
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
purge haplotigs 1.0 module load purge_haplotigs/1.0
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
tombo 1.5 module load tombo/1.5
unicycler 0.4.7 module load unicycler/0.4.7
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 
gcta 1.92.1beta6 module load gcta/1.92.1beta6
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
ldsc 1.0.0 module load ldsc/1.0.0
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
Kraken2 2.0.8-beta module load kraken/2.0.8-beta
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 1.42.1 module load mothur/1.42.1
qiime 2-2018.8 module load qiime/2-2018.8
rnammer 1.2 module load rnammer/1.2
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 1.6.10 module load iqtree/1.6.10
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/2.2.7
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
q2-picrust 0.0.3 module load q2-picrust2/0.0.3
RAxML 8.2.11 module load RAxML/8.2.11
raxml-ng 0.7.0 module load raxml-ng/0.7.0
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-LMM/2.3.2
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 2.4 module load stacks/2.4

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
$BLASTDB
Blat 36×2 module load Blat/36×2
BRAKER 2.1.2 module load BRAKER/2.1.2
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
CRISPRdigger 1.007 module load CRISPRdigger/1.007
DIAMOND 0.9.24 module load diamond/0.9.24
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
hh-suite 3.2.0 module load hh-suite/3.2.0
HMMER 3.2.1 module load hmmer/3.2.1
Infernal 1.1.1 module load infernal/1.1.1
InterProScan 5.35-74.0 module load interproscan/5.35-74.0
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 1.13 module load prokka/1.13
seaview 4.7 module load seaview/4.7
SeqKit 0.10.0 module load seqkit/0.10.0
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
speedseq 0.1.2 module load speedseq/0.1.2
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
guppy 2.3.1 module load guppy/2.3.1
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 1.7 module load MultiQC/1.7
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
tsl 1.23 module load tsl/1.23
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 3.6.0 module load R/3.6.0
RStan
Bioconductor 3.8, IRanges, GenomicRanges, DESeq2, dplyr, gplots, ggplot2, RColorBrewer, genefilter
interactive session: Rscript <your_script.R>
sbatch script: R CMD BATCH <your_script.R>
Rstan 3.5.2 module load R/3.5.2

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
cellranger-dna 1.0.0 module load cellranger-dna/1.0.0
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/0.9.0-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 1.3.6 module load stringtie/1.3.6
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
NanoPack 1.0.1 module load nanopack/1.0.1
NanoPlot 1.21.0 module load NanoPlot/1.21.0