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 |