Architecture: x86_64
Operating System: CENTOS 7.7-1908
Cluster scheduler: SLURM 18.08.02
Parallel libraries: OpenMPI 3.1.2 and PMIx 3.0.2




Packages installed
Package Version Description Install
Abaqus 6.1.4 Engineering simulation software software/abaqus-6.14
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
bamtools 2.5.1 Toolkit for handling BAM files. module load software/bamtools-2.5.1
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 1.10.4 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 2.4.1 Tool for aligning sequencing reads to long reference sequences module load software/bowtie2-2.4.1
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 3.1.0 Pipeline for analysing single cell 3' RNA-seq data module load software/cellranger-3.1.0
cmake 3.12.4 software packaging and building tools module load tools/cmake-3.12.4
diamond 2.0.1 Sequence aligner for protein and translated DNA searches module load software/diamond-2.0.1
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 0.11.8 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
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 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 8.2.0 Gnu compiler - C and Fortran module load compilers/gcc820
gnuParallel 20190722 Shell tool for executing jobs in parallel - CONTACT HPC ADMINS BEFORE USING!!! module load software/gnu-parallel-20190722
Gromacs 2019.1 Molecular dynamics module load software/Gromacs-2019.1
Guppy 3.2.4 Guppy is a data processing Oxford Nanopore Technologies module load software/ont-guppy
htslib NA Tool for accessing common file formats for high-throughput sequencing data module load tools/htslib
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
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
Java 11 Java language development kit module load java/jdk-11
Java 8 Java language development kit module load java/jdk-8
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
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 12.0 Technical computing module load software/mathematica-12.0
Matlab R2020b Matlab base package module load software/matlab-R2020b
Matlab R2020b Parallel Server Run from desktop
Matlab R2020b All Toolboxes Run from matlab
Matlab R2019b Matlab base package module load software/matlab-R2019b
Matlab R2019b Parallel Server Run from desktop
Matlab R2019b All Toolboxes Run from matlab
miniconda 3.7 Miniconda version of python module load python/miniconda3
mpich 3.3 Message Passing Interface for parallel software module load mpi/mpich-3.3
Mono 6.8.0 Cross platform application development all worker nodes
Monolix 2019R1 Mixed effects modeling for pharmacometrics Pharmacology group only
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 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 4.0.1 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
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
plink 1.07 Whole genome association analysis toolset module load software/plink-1.07
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 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 4.0.1 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 1.2.1 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 1.9 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
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 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
Stata 13 Statistics Graphics and Data Management module load software/stata-13
TensorFlow 1.12 CPU version Machine learning framework module load software/TensorFlow-CPU-py2 or 3
TensorFlow 1.12 GPU version Machine learning framework module load software/TensorFlow-GPU-py2 or 3
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
Trimmomatic 0.39 A flexible read trimming tool for Illumina NGS data module load software/Trimmomatic-0.39
Trinity 2.10.0 RNA-Seq de novo transcriptome assembly module load software/trinity-2.10.0
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