Software installed on the clusters is available for public use without restriction. Users must be comfortable in a Unix environment and understand how to properly submit jobs. The Xanadu cluster is replacing the BBC cluster for research use. 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
All softwares listed current as of 06/10/2019
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 |