| Packages installed | |||
| Package | Version | Description | Install |
| Abaqus | 6.1.4 | Engineering simulation software | module load software/abaqus-6.14 |
| Angsd | 0.94 | NGS analysis | module load software/angsd-0.94 |
| Annovar | 2018-04 | Functional annotation of genetic variants from high-throughput sequencing data | /opt/exp_soft/annovar-2018-04 |
| AnsysEM | 2020R2 | Electromagnetic | /opt/exp_soft/ansys_inc/AnsysEM20.2 |
| AnsysEM | 19.3 | Electromagnetic | /opt/exp_soft/ansys_inc/AnsysEM19.3 |
| AnsysEM | 19.2 | Electromagnetic | /opt/exp_soft/ansys_inc/AnsysEM19.2 |
| AnsysFluent | 2020R2 | CFD package | /opt/exp_soft/ansys_inc/v202 |
| AnsysFluent | 19.3 | CFD package | /opt/exp_soft/ansys_inc/v193 |
| AnsysFluent | 19.2 | CFD package | /opt/exp_soft/ansys_inc/v192 |
| AnsysFluent | 19.1 | CFD package | /opt/exp_soft/ansys_inc/v191 |
| AnsysFluent | 15.7 | CFD package | /opt/exp_soft/ansys_inc/v150 |
| Astral | 5.6.3 | Unrooted species tree estimation | module load software/Astral-5.6.3 |
| Alphafold | v2.0 | Inference Software | /opt/exp_soft/singularity-containers/alphafold/alphafold.sif |
| bamtools | 2.5.1 | Toolkit for handling BAM files. | module load software/bamtools-2.5.1 |
| BBMap | 38.96 | Splice-aware global aligner for DNA and RNA sequencing reads | software/bbmap-38.96 |
| bcftools | 1.19 | Flexible generic format for storing nucleotide sequence alignment | module load software/bcftools-1.19 |
| bcftools | 1.9 | Flexible generic format for storing nucleotide sequence alignment | module load software/bcftools-1.9 |
| bcl2fastq | 2.2.0 | Demultiplexes sequencing data and converts BCL files into FASTQ files | module load software/bcl2fastq2-v2.20 |
| BEAGLE | 3.2.0 | Bayesian library for BEAST | via BEAGLE |
| BEAST | 1.10.5pt | Phylogenetic analysis with an emphasis on time-scaled trees | module load software/BEASTv1.10.5pre_thorney_0.1.1 |
| BEAST | 1.10.4 | Phylogenetic analysis with an emphasis on time-scaled trees | module load software/beast-1.10.4 |
| BEAST | 1.8.4 | Phylogenetic analysis with an emphasis on time-scaled trees | module load software/beast-1.8.4 |
| bedtools | 2.29 | Genome arithmetic | module load software/bedtools-2.29 |
| bowtie2 | 2.4.5 | Tool for aligning sequencing reads to long reference sequences | module load software/bowtie2-2.4.5 |
| bowtie2 | 2.4.1 | Tool for aligning sequencing reads to long reference sequences | module load software/bowtie2-2.4.1 |
| bowtie | 0.12.9 | Short read aligner | module load software/bowtie-0.12.9 |
| BWA | 0.7.17 | Burrows-Wheeler Aligner is a program for aligning sequencing reads against a large reference genome | module load software/bwa-0.7.17 |
| cdo | 1.9.6 | Climate Data Operators | module load software/cdo-1.9.6 |
| CellRanger | 7.2.0 | Pipeline for analysing single cell 3' RNA-seq data | module load software/cellranger-7.2.0 |
| CellRanger | 6.0.1 | Pipeline for analysing single cell 3' RNA-seq data | module load software/cellranger-6.0.1 |
| CellRanger | 3.1.0 | Pipeline for analysing single cell 3' RNA-seq data | module load software/cellranger-3.1.0 |
| CellRanger-atac | 2.0.0 | Pipelines for processing Chromium Single Cell ATAC data | module load software/cellranger-atac-2.0.0 |
| cmake | 3.12.4 | software packaging and building tools | module load tools/cmake-3.12.4 |
| Canu | 2.2 | Designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION | module load software/canu-2.2 |
| Dask | 8.1 | Advanced parallelism for analytics in Python 3.9.5 | module load python/miniconda3-dask |
| diamond | 2.0.1 | Sequence aligner for protein and translated DNA searches | module load software/diamond-2.0.1 |
| diamond | 2.0.13 | Sequence aligner for protein and translated DNA searches | module load software/diamond-2.0.13 |
| dorado | 0.3.4 | Basecaller for Oxford Nanopore reads | module load software/dorado-0.3.4 |
| dorado | 0.1.1 | Basecaller for Oxford Nanopore reads | module load software/dorado-0.1.1 |
| emboss | 6.6.0 | Open source software tools for molecular biology | module load software/emboss-6.0.0 |
| ESyS-Particle | 3.0b | Particle-based numerical modelling | module load software/ESyS-Particle-3.0b |
| ESyS-Particle | 2.3.5 | Particle-based numerical modelling | module load software/ESyS-Particle-2.3.5 |
| exonerate | 2.2.0 | Pairwise sequence comparisons | module load software/exonerate-2.2.0 |
| express | 1.5.1 | Streaming fragment assignment and quantification for high-throughput sequencing | module load express-1.5.1 |
| FastQC | 0.11.9 | Quality control application for high throughput sequence data | module load software/FastQC-0.11.9 |
| FastQC | 0.11.8 | Quality control application for high throughput sequence data | module load software/FastQC-0.11.8 |
| fftw | 3.3.8 | Fast Fourier Transform library | module load tools/fftw-3.3.8 |
| fiji | 1.53c | Image processing package | module load software/Fiji.app-1.53c |
| FreeBayes | 1.3.6 | Bayesian haplotype-based genetic polymorphism discovery and genotyping | module load software/freebayes-1.3.6 |
| FreeBayes | 1.2.0 | Bayesian haplotype-based genetic polymorphism discovery and genotyping | module load software/freebayes-1.2.0 |
| FreeSurfer | 7.2.0 | Structural and Functional Neuroimaging data | module load software/freesurfer-7.2.0 |
| FreeSurfer | 6.0.1 | Structural and Functional Neuroimaging data | module load software/freesurfer-6.0.1 |
| FreeSurfer | 5.3.0 | Structural and Functional Neuroimaging data | module load software/freesurfer-5.3.0 |
| Gaussian | 16-C.01 | General purpose computational chemistry software | module load software/gaussian-16-C.01 |
| Gaussian | 9.0 | General purpose computational chemistry software | module load software/gaussian-09 |
| gatk | 4.1.2.0 | The Genome Analysis Toolkit | module load software/gatk-4.1.2.0 |
| gcc | 11.2 | Gnu compiler - C and Fortran | module load compilers/gcc11.2 |
| gcc | 10.3 | Gnu compiler - C and Fortran | module load compilers/gcc10.3 |
| gcc | 8.2.0 | Gnu compiler - C and Fortran | module load compilers/gcc820 |
| geos | 13.10.2 | Geospatial software | module load software/geos-3.10.2 |
| gffread | 0.12.7 | Format conversions filtering FASTA sequence extraction and more | module load software/gffread-0.12.7 |
| giggle | 0.6.3 | Genomics search engine | module load software/giggle-0.6.3 |
| Git | 2.32 | Git version control | module load software/git-2.32 |
| gnuParallel | 20190722 | Shell tool for executing jobs in parallel - CONTACT HPC ADMINS BEFORE USING!!! | module load software/gnu-parallel-20190722 |
| Go | 1.16.2 | Open source programming language | module load compilers/go-1.16.2 |
| Gromacs | 2019.1 | Molecular dynamics | module load software/Gromacs-2019.1 |
| Guppy | 6.5.7 | ONT Basecaller - GPU | module load software/ont-guppy-6.5.7 |
| Guppy | 6.5.7 | ONT Basecaller - CPU | module load software/ont-guppy-cpu-6.5.7 |
| Guppy | 3.2.4 | ONT Basecaller - GPU | module load software/ont-guppy |
| Guppy | 3.2.4 | ONT Basecaller - CPU | module load software/ont-guppy-cpu |
| hisat2 | 2.2.1 | Graph-based alignment of next generation sequencing reads | module load software/hisat2-2.2.1 |
| htslib | 1.19.1 | Tool for accessing common file formats for high-throughput sequencing data | module load tools/htslib-1.19.1 |
| htslib | NA | Tool for accessing common file formats for high-throughput sequencing data | module load tools/htslib |
| hmmer | 3.3.2 | Biosequence analysis using profile hidden Markov models | module load software/hmmer-3.3.2 |
| hmmer | 3.3.1 | Biosequence analysis using profile hidden Markov models | module load software/hmmer-3.3.1 |
| HyPhy | 2.5.0 | Hypothesis testing using Phylogenies | module load software/HyPhy-2.5.0 |
| HyPhy | 2.3.14 Beta | Hypothesis testing using Phylogenies | module load software/HyPhy-2.3.14B |
| HyPhy | 2.3.12 | Hypothesis testing using Phylogenies | module load software/HyPhy-2.3.12 |
| HyPhy | 2.3.5 | Hypothesis testing using Phylogenies | module load software/HyPhy-2.3.5 |
| ilastik | 1.3.3 | Interactive learning and segmentation toolkit | module load software/ilastik-1.3.3 |
| iqtree | 2.1.3 | Stochastic algorithm to infer phylogenetic trees by maximum likelihood COVID-19 release | module load software/iqtree-2.1.3 |
| iqtree | 2.0.4 | Stochastic algorithm to infer phylogenetic trees by maximum likelihood | module load software/iqtree-2.0.4 |
| iqtree | 1.6.11 | Stochastic algorithm to infer phylogenetic trees by maximum likelihood | module load software/iqtree-1.6.11 |
| jags | 4.3.0 | Bayesian hierarchical model analysis | module load software/jags-4.3.0 |
| Java | 17 | Java language development kit | module load java/jdk-17 |
| Java | 11 | Java language development kit | module load java/jdk-11 |
| Java | 8 | Java language development kit | module load java/jdk-8 |
| Julia | 1.9.4 | Julia compiler | module load compilers/julia-1.9.4 |
| Julia | 1.5.2 | Julia compiler | module load compilers/julia-1.5.2 |
| Julia | 1.1.1 | Julia compiler | module load compilers/julia-1.1.1 |
| kallisto | 0.44 | Quantifying abundances of transcripts from RNA-Seq data | module load software/kallisto-0.44 |
| kSNP | 3.1 | Identifies the pan-genome SNPs in a set of genome sequences | module load software/kSNP3.1 |
| ls-dyna | v222 | Finite element simulation | module load software/ls-dyna-ansys |
| ls-dyna | 10.1.0 | Finite element simulation | module load software/ls-dyna-10.1.0 |
| ls-dyna | 8.1.0 | Finite element simulation | module load software/ls-dyna-8.1.0 |
| mafft | 7.427 | Multiple sequence alignment program for unix-like operating systems | module load software/mafft-7.427 |
| Mathematica | 12.3 | Technical computing | module load software/mathematica-12.3 |
| Matlab | R2022b | Matlab base package | module load software/matlab-R2022b |
| Matlab | R2021b | Matlab base package | module load software/matlab-R2021b |
| Matlab | R2020b | Matlab base package | module load software/matlab-R2020b |
| Matlab | R2019b | Matlab base package | module load software/matlab-R2019b |
| MaxQuant | 2.0.3.0 | Quantitative proteomics software package | module load software/MaxQuant-2.0.3.0 (run with dotnet) |
| MaxQuant | 1.6.14 | Quantitative proteomics software package | module load software/MaxQuant-1.6.14 (run with dotnet) |
| medusa | 1.6 | A draft genome scaffolder | module load medusa-1.6 |
| metal | 2011-03-25 | Meta-analysis of large whole genome datasets | module load software/metal-2011-03-25 |
| miniconda | 3.10 | Miniconda version of python 3.10.11 | module load python/miniconda3-py310 |
| miniconda | 4.11.0 | Miniconda version of python 3.9.5 with user libraries | module load python/miniconda3-py3.9-usr |
| miniconda | 4.9.2 | Miniconda version of python 3.9.5 | module load python/miniconda3-py3.9 |
| miniconda | 4.9.2 | Miniconda version of python 3.9.5 | module load python/miniconda3-py3.9 |
| miniconda | 3.7 | Miniconda version of python 2.6 | module load python/miniconda3 |
| Mono | 6.8.0 | Cross platform application development | all worker nodes |
| Monolix | 2019R1 | Mixed effects modeling for pharmacometrics | Pharmacology group only |
| Mothur | 14.5.3 | Software to analyze community sequence data | module load software/mothur-14.5.3 |
| MotifBinner2 | 2.0 | MotifBinner processes high-throughput sequencing data of an RNA virus population | Singularity Container |
| mpich | 3.3 | Message Passing Interface for parallel software | module load mpi/mpich-3.3 |
| msdial | 4.70 | Untargeted metabolomics and lipidomics | software/msdial-4.70 |
| MUMmer | 3.23 | Rapid alignment of entire genomes | module load mummer-3.2.3 |
| NAMD | 2.14 | Molecular dynamics simulation package | module load software/NAMD-2.14-CUDA |
| NAMD | 2.13 | Molecular dynamics simulation package | module load software/NAMD-2.13-CUDA |
| NAMD | 2.12 | Molecular dynamics simulation package | module load software/NAMD-2.12-CUDA |
| NAMD | 2.11 | Molecular dynamics simulation package | module load software/NAMD-2.11-CUDA |
| ncbi-blast | 2.9.0 | Basic Local Alignment Search Tool | module load software/ncbi-blast-2.9.0 |
| ncview | 2.1.7 | Visual browser for netcdf files | module load software/ncview-2.1.7 |
| ncview | 2.1.2 | Visual browser for netcdf files | all worker nodes |
| NetCDF-c | 4.6.3 | Network Common Data Form | module load software/netcdf-c-4.6.3 |
| NetCDF-fortran | 4.6.3 | Network Common Data Form | module load software/netcdf-fortran-4.4.5 |
| Nextflow | 23.04.3 | Data-driven computational pipeline | module load software/nextflow-23.04.3 |
| Nextflow | 21.10.6 | Data-driven computational pipeline | module load software/nextflow-21.10.6 |
| Nextflow | 21.04.3 | Data-driven computational pipeline | module load software/nextflow-21.04.3 |
| Nextflow | 20.04 | Data-driven computational pipeline | module load software/nextflow-20.04 |
| Nextflow | 19.04 | Data-driven computational pipeline | module load software/nextflow-19.04 |
| Octave | 4.4.1 | High-level interpreted language for numerical computations | module load software/octave-4.4.1 |
| OpenMPI | 4.1.0 | Message Passing Interface for parallel software with gcc11.2 | module load mpi/openmpi-4.1.0 |
| OpenMPI | 4.1.0 | Message Passing Interface for parallel software. For use on sadacc partitions only! | module load mpi/openmpi-4.0.1-sadacc |
| OpenMPI | 4.0.1 | Message Passing Interface for parallel software | module load mpi/openmpi-4.0.1 |
| OpenMPI | 3.1.2 | Message Passing Interface for parallel software | module load mpi/openmpi-3.1.2 |
| OpenMPI | 1.10.7 | Message Passing Interface for parallel software | module load mpi/openmpi-1.10.7 |
| OpenMPI | 1.8.3 | Message Passing Interface for parallel software | module load mpi/openmpi-1.8.3 |
| paml | 4.9h | Phylogenetic analyses of DNA or protein sequences | module load software/paml-4.9h |
| paraview | 5.10.1 | Data analysis and visualization application | module load software/Paraview-5.10.1 |
| perl | 5.28.0 | Perl scripting language | module load compilers/perl-5.28 |
| perl | 5.16.3 | Perl scripting language | all worker nodes |
| perl | 5.10.1 | Perl scripting language | module load compilers/perl-5.10 |
| picard | 2.20.1 | Java-based command-line utilities that manipulate SAM files | /opt/exp_soft/picard-2.20.1 |
| PICRUSt2 | 2.5.0 | Phylogenetic Investigation of Communities by Reconstruction of Unobserved STates | module load python/miniconda3-py39-picrust2 |
| plink | 2.00 alpha | Whole genome association analysis toolset | module load software/plink-2.00a |
| plink | 1.90 beta | Whole genome association analysis toolset | module load software/plink-1.90b |
| plink | 1.07 | Whole genome association analysis toolset | module load software/plink-1.07 |
| prodigal | 2.6.3 | Protein-coding gene prediction for prokaryotic genomes | module load software/prodigal-2.6.3 |
| Python | 2.7.14 | Anaconda version of python | module load python/anaconda-python-2.7 |
| Python | 3.7.1 | Anaconda version of python | module load python/anaconda-python-3.7 |
| Quantum Espresso | 7.0.0 | Electronic-structure calculations and materials modeling at the nanoscale | module load software/qe-7.0.0 |
| Quantum Espresso | 6.4.1 | Electronic-structure calculations and materials modeling at the nanoscale | module load software/qe-6.4.1 |
| QIIME 2 | 2020.8 | Microbiome analysis package | module load python/miniconda3-qiime2 |
| R | 4.2.0 | Statistical computing and graphics with many bioconductor packages etc | module load software/R-4.2.0-HL |
| R | 4.2.0 | Statistical computing and graphics | module load software/R-4.2.0 |
| R | 4.1.1 | Statistical computing and graphics | module load software/R-4.1.1 |
| R | 4.0.5 | Statistical computing and graphics | module load software/R-4.0.5 |
| R | 4.0.1 | Statistical computing and graphics | module load software/R-4.0.1 |
| R | 3.6.0 | Statistical computing and graphics | module load software/R-3.6.0 |
| R | 3.5.3 | Statistical computing and graphics | module load software/R-3.5.3 |
| R | 3.5.2 | Statistical computing and graphics | module load software/R-3.5.2 |
| R | 3.5.1 | Statistical computing and graphics | module load software/R-3.5.1 |
| RAxML | 8.2 | Maximum Likelihood based inference of large phylogenetic trees | module load software/RAxML-8.2 |
| RSEM | 1.3.3 | Accurate quantification of gene and isoform expression from RNA-Seq data | module load software/RSEM-1.3.3 |
| salmon | 1.6.0 | Transcript quantification from RNA-seq data | module load software/salmon-1.6.0 |
| salmon | 1.2.1 | Transcript quantification from RNA-seq data | module load software/salmon-1.2.1 |
| salmon | 1.2.0 | Transcript quantification from RNA-seq data | module load software/salmon-1.2.0 |
| samtools | 1.14 | Flexible generic format for storing nucleotide sequence alignment | module load software/samtools-1.14 |
| samtools | 1.9 | Flexible generic format for storing nucleotide sequence alignment | module load software/samtools-1.9 |
| Scala | 2.12.8 | Multi-paradigm programming language | module load compile/scala-lang |
| Singularity | 3.0.1 | Containerization environment | all worker nodes |
| snap | 9.0 | Earth Observation processing | module load software/snap-9.0 |
| snap | 8.0 | Earth Observation processing | module load software/snap-8.0 |
| snpEff | 4.3 | Fast variant effect predictor for genomic data | /opt/exp_soft/snpEff-4.3/ |
| SortaDate | NA | Genetic analysis | module load software/sorta |
| SPAdes | 3.13.0 | St. Petersburg genome assembler | software/SPAdes-3.13.0 |
| SRAtoolkit | 3.0.0 | A collection of tools and libraries for using data in the INSDC Sequence Read Archives | module load software/sratoolkit-3.0.0 |
| SRAtoolkit | 2.9.6 | A collection of tools and libraries for using data in the INSDC Sequence Read Archives | module load software/sratoolkit-2.9.6 |
| STAR | 2.7.9a | Spliced Transcripts Alignment to a Reference | module load software/star-2.7.9a |
| Stata | 13 | Statistics Graphics and Data Management | module load software/stata-13 |
| Sprai | 0.9.1 | Genome Assembly | module load software/sprai-0.9.3 |
| subread | 2.0.3 | Next-gen sequencing read data processing | module load software/subread-2.0.3 |
| TensorFlow | 1.12 CPU version | Machine learning framework | module load software/TensorFlow-1x-GPU |
| TensorFlow | 1.12 GPU version | Machine learning framework | module load software/TensorFlow-2x-GPU |
| Texlive/Latex | 2020 | TeX typesetting system | module load software/texlive2020 |
| TransDecoder | 5.5.0 | Find Coding Regions Within Transcripts | module load software/TransDecoder-v5.5.0 |
| trimAL | 1.2 | Automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment | module load software/trimAL-1.2 |
| TrimGalore | 0.6.8 | Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files | module load software/TrimGalore-0.6.8 |
| TrimGalore | 0.6.6 | Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files | module load software/TrimGalore-0.6.6 |
| Trimmomatic | 0.39 | A flexible read trimming tool for Illumina NGS data | module load software/Trimmomatic-0.39 |
| Trinity | 2.13.2 | RNA-Seq de novo transcriptome assembly | module load software/trinity-2.13.2 |
| Trinity | 2.10.0 | RNA-Seq de novo transcriptome assembly | module load software/trinity-2.10.0 |
| Trinotate | 3.2.2 | Transcriptome and protein data search | module load software/Trinotate-v3.2.2 |
| Trinotate | 3.2.1 | Transcriptome and protein data search | module load software/Trinotate-v3.2.1 |
| varscan | 2.3.9 | Variant detection in massively parallel sequencing | /opt/exp_soft/varscan-2.3.9 |
| vcflib | NA | C++ library and cmdline tools for parsing and manipulating VCF files | module load software/vcflib |
| vcftools | 0.1.16 | Maps short reads to a reference genome | module load software/vcftools-0.1.16 |
| VMD | 1.9.3 | Visual Molecular Dynamics | module load software/vmd-1.9.3 |
| VMSI | NA | VMSI MicroCosm | module load software/vmsi |
| Wannier90 | 3.1.0 | Generate maximally-localized Wannier functions | module load software/wannier90-3.1.0 |
| WGS-Assembler | 8.3 | Whole-Genome Shotgun Assembler | module load software/wgs-assembler |