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 Module 
Bismark module load bismark/
macs module load macs/
macs2 module load macs2/
NucleoATAC module load NucleoATAC/
peakSplitter module load peakSplitter/

Data Transfer

Software Module 
BaseMount module load basemount/
BaseSpaceCLI module load basespace-cli/
edirect module load edirect/
GDC_Data_Transfer_Tool module load GDC_Data_Transfer_Tool/
gdrive module load gdrive/
sratoolkit module load sratoolkit/

Database

Software Module 
postgresql module load postgresql-client/
sqlite module load sqlite/

Genome Assembly

Software Module 
abyss module load abyss/
AlignGraph module load AlignGraph/
AMOS module load AMOS/
CAMSA module load camsa/
Canu module load canu/
CAP3 module load CAP3/
DISCOVAR de novo module load DiscovarDeNovo/
flye module load flye/
GapFiller module load GapFiller/
GMcloser module load GMcloser/
Jellyfish module load jellyfish/
MaSuRCA module load MaSuRCA/
Metassembler module load Metassembler/
nanocorrect module load nanocorrect/
nanopolish module load nanopolish/
pandaseq module load pandaseq/
Phrap module load phrap/
pilon module load pilon/
Platanus module load Platanus/
platanus-allee module load platanus-allee/
purge haplotigs module load purge_haplotigs/
quast module load quast/
racon module load racon/
Ray module load Ray/
SOAP-denovo module load SOAP-denovo/
SPAdes module load SPAdes/
SSPACE-LongRead module load SSPACE-LongRead/
SSPACE-Standard module load SSPACE/
tombo module load tombo/
unicycler module load unicycler/
velvet module load velvet/
Phred module load phred/

Genome Wide Methods

Software Module 
gcta module load gcta/
HiC-Pro module load HiC-Pro/
ISseeker module load ISseeker/
juicer module load juicer/
ldsc module load ldsc/
w4cseq module load w4cseq/

Metagenomics

Software Module 
bracken module load bracken/
CONCOCT module load CONCOCT/
FragGeneScan module load FragGeneScan/
HUMAnN2 module load humann2/
Kraken module load kraken/
Kraken2 module load kraken/
mash module load mash/
MaxBin module load MaxBin/
megahit module load megahit/
MetaBAT module load metabat/
MetaCRAST module load MetaCRAST/
MetaVelvet module load MetaVelvet/
microbiomeutil module load microbiomeutil/
MinCED module load MinCED/
mothur module load mothur/
qiime module load qiime/
rnammer module load rnammer/
SortMeRNA module load sortmerna/

Phylogenetics

Software Module 
CAFÉ module load CAFE/
CheckM module load CheckM/
clearcut module load clearcut/
FastME module load FastME/
FastTree module load fasttree/
GARLI module load garli/
HyPhy module load hyphy/
IQ-TREE module load iqtree/
mashtree module load mashtree/
mauve module load mauve/
MetaPhlAn module load MetaPhlAn/
Migrate-n module load migrate/
MrBayes module load MrBayes/
OrthoFinder module load OrthoFinder/
PAML module load paml/
PAUP* module load paup/
phylip module load phylip/
PhyloSift module load PhyloSift/
PhyML module load PhyML/
pplacer module load pplacer/
q2-picrust module load q2-picrust2/
RAxML module load RAxML/
raxml-ng module load raxml-ng/
scythe module load scythe/
tree-puzzle module load tree-puzzle/
treeFix-DTL module load treefixDTL/

Population Genetics

Software Module 
arlecore module load arlecore/
arlsumstat module load arlsumstat/
BAPS module load BAPS/
BayesAss module load BayesAss/
BOLT-LMM module load BOLT-LMM/
fastStructure module load fastStructure/
qctool module load qctool/
RefineM module load refinem/
structure module load structure/

Proteomics

Software Module 
omssa module load omssa/
PeptideShaker module load PeptideShaker/

RAD-Seq

Software Module 
dDocent module load dDocent/
ipyrad module load ipyrad/
pyrad module load pyrad/
rainbow module load rainbow/
stacks module load stacks/

Repeat Identification

Software Module 
CRISPRDetect module load CRISPRDetect/
RECON module load RECON/
RepeatMasker module load RepeatMasker/
RepeatModeler module load RepeatModeler/
RepeatScout module load RepeatScout/
rmblastn module load rmblastn/
Sputnik module load sputnik/
TRF module load TRF/

RNA Structure

Software Module 
LocARNA module load locarna/
RNAz module load RNAz/
reapr module load reapr/

Sequence Alignment/Annotation

Software Module 
antiSMASH module load antiSMASH/
aragorn module load aragorn/
Augustus module load augustus/
bamtools module load bamtools/
BARRNAP module load barrnap/
bedtools module load bedtools/
BEDtools module load BEDtools/
blast module load blast/
Blat module load Blat/
BRAKER module load BRAKER/
busco module load busco/
CD-HIT module load cdhit/
clustalw module load clustalw/
CRISPRdigger module load CRISPRdigger/
DIAMOND module load diamond/
eggnog-mapper module load eggnog-mapper/
ELPH module load elph/
emboss module load emboss/
EVidenceModeler module load EVidenceModeler/
Exonerate module load exonerate/
fastmiso module load fastmiso/
gemma module load gemma/
genomethreader module load genomethreader/
GenomeTools module load genometools/
GET_HOMOLOGUES module load get_homologues/
gffcompare module load gffcompare/
gffread module load gffread/
glimmerhmm module load glimmerhmm/
gridss module load gridss/
hh-suite module load hh-suite/
HMMER module load hmmer/
Infernal module load infernal/
InterProScan module load interproscan/
last module load last/
legacy-blast module load legacy-blast/
MAFFT module load mafft/
MAKER module load maker/
meme module load meme/
minimap2 module load minimap2/
miso module load miso/
MISO module load MISO/
MUMmer module load MUMmer/
MUSCLE module load muscle/
PASApipeline module load PASApipeline/
PBSuite module load PBSuite/
pear module load pear/
PrAS module load PrAS/
prodigal module load prodigal/
prokka module load prokka/
seaview module load seaview/
SeqKit module load seqkit/
seqtools module load seqtools/
signalp module load signalp/
snap module load snap/
SNP2HLA module load SNP2HLA/
spaln module load spaln/
speedseq module load speedseq/
subread module load subread/
taco module load taco/
uclust module load uclust/
ucsc_genome module load ucsc_genome/
usearch module load usearch/
vsearch module load vsearch/
yaha module load yaha/
Glimmer module load glimmer/

Short Read Alignment and Quality Control

Software Module 
AfterQC module load AfterQC/
AmpliconNoise module load AmpliconNoise/
autobarcode module load autobarcode/
bamutil module load bamutil/
BBMap module load bbmap/
bcl2fastq module load bcl2fastq/
BFAST module load bfast/
bowtie module load bowtie/
bowtie2 module load bowtie2/
BWA module load bwa/
cdbtools module load cdbtools/
FastQC module load fastqc/
FASTX-Toolkit module load fastx/
flexbar module load flexbar/
GMAP module load gmap/
graphmap module load graphmap/
guppy module load guppy/
HISAT2 module load hisat2/
htseq module load htseq/
mirdeep2 module load mirdeep2/
MultiQC module load MultiQC/
NxTrim module load NxTrim/
picard module load picard/
poretools module load poretools/
pysam module load pysam/
qualimap module load qualimap/
samblaster module load samblaster/
samtools module load samtools/
seqtk module load seqtk/
sickle module load sickle/
tabix module load tabix/
tbl2asn module load tbl2asn/
Trimmomatic module load Trimmomatic/
java -jar $Trimmomatic
tsl module load tsl/
XSQ_Tools module load XSQ_Tools/
cutadapt module load cutadapt/
deepTools module load deeptools/
DLCpar module load DLCpar/
DWGSIM module load DWGSIM/
ea-utils module load ea-utils/
CompareM module load CompareM/

Statistics

Software Module 
R module load R/
R module load R/
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 module load R/

Structure Calculations and Modeling

Software Module 
Gaussian module load gaussian/
Gromacs module load Gromacs/
QuantumEspresso module load QuantumEspresso/
randfold module load randfold/
ViennaRNA module load ViennaRNA/
vina module load vina/

Transcriptomics

Software Module 
bcftools module load bcftools/
Cell Ranger module load cellranger/
cellranger-dna module load cellranger-dna/
Cufflinks module load cufflinks/
DETONATE module load detonate/
EDGE-pro module load EDGE_pro/
EnTAP module load EnTAP/
eXpress module load express/
FrameDP module load FrameDP/
GeneMark-ET module load GeneMark-ET/
gfold module load gfold/
HTSeq module load htseq/
idba module load idba/
isoem2 module load isoem2/
jsplice module load jsplice/
Kallisto module load kallisto/
KisSplice module load kissplice/
mats module load mats/
miARma module load miARma/
mira module load mira/
rail-rna module load rail-rna/
REDItools module load reditools/
rMATS module load rMATS/
rsem module load rsem/
salmon module load salmon/
STAR module load STAR/
stringtie module load stringtie/
suppa module load suppa/
tophat module load tophat/
Trans-ABySS module load transabyss/
TransDecoder module load TransDecoder/
transrate module load transrate/
Trinity module load trinity/
Trinotate module load Trinotate/

Variant Detection

Software Module 
CASAVA module load casava/
DISCOVAR module load Discovar/
EXCAVATOR2 module load EXCAVATOR2/
FreeBayes module load freebayes/
GATK module load GATK/
hap.py module load hap.py/
IMPUTE2 module load impute2/
Long Ranger module load longranger/
marginAlign module load marginAlign/
MuTect module load MuTect/
pindel module load pindel/
plink module load plink/
pyvcf module load pyvcf/
rtg-tools module load rtg-tools/
snpEff module load snpEff/
SNPGenie module load SNPGenie/
snptest module load snptest/
varscan module load varscan/
vcflib module load vcflib/
vcftools module load vcftools/

Visualization

Software Module 
circos module load circos/
consed module load consed/
FreeSurfer module load FreeSurfer/
FSL module load FSL/
GenomeBrowser module load GenomeBrowser/
imageMagick module load imageMagick/
ITK-SNAP module load ITK-SNAP/
majiq module load majiq/
NanoPack module load nanopack/
NanoPlot module load NanoPlot/