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 |