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:
- ChIP-Seq / Methyl-Seq Analysis
- Data Transfer
- Database
- Genome Assembly
- Genome Wide Methods
- Metagenomics
- Phylogenetics
- Population Genetics
- Proteomics
- RAD-Seq
- Repeat Identification
- RNA Structure
- Sequence Alignment/Annotation
- Short Read Alignment and Quality Control
- Statistics
- Structure Calculations and Modeling
- Transcriptomics
- Variant Detection
- Visualization
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/ |