Biosciences, Bioinformatics and Biomedicine

Name

Links

Category

Restricted License

GPU Acceleration

Abyss

Homepage

Install with bioconda

High-Throughput
Sequencing

    

Adam

Homepage

Install with bioconda

High-Throughput
Sequencing

    

Bowtie2

Homepage

Install with bioconda

High-Throughput
Sequencing

    

Burrow-Wheeler
Aligner

Homepage

Install with bioconda

High-Throughput
Sequencing

    

Delly

Homepage

Install with bioconda

High-Throughput
Sequencing

    

Fastp

Homepage

Install with bioconda

High-Throughput
Sequencing

    

GATK3

Homepage

Install with bioconda

High-Throughput
Sequencing

    

GATK4

Homepage

Install with bioconda

High-Throughput
Sequencing

    

Pear

Homepage

Install with bioconda

High-Throughput
Sequencing

    

Sambamba

Homepage

Install with bioconda

High-Throughput
Sequencing

    

Selscan

Homepage

Install with bioconda

High-Throughput
Sequencing

    

Beagle-lib

Homepage

Install with bioconda

Linkage/
Phylogenetics

    

RAxML

Homepage

Install with bioconda

Linkage/
Phylogenetics

    

Maxquant

Homepage

Install with bioconda

Mass Spectrometry

Maxquant Freeware Software License

  

Autodock-vina

Homepage

Install with bioconda

Molecular Docking

    

Blast

Homepage

Install with bioconda

Sequence Analysis

    

Diamond

Homepage

Install with bioconda

Sequence Analysis

    

Magicblast

Homepage

Install with bioconda

Sequence Analysis

    

Meme

Homepage

Install with bioconda

Sequence Analysis

    

rDock

Homepage

Install with bioconda

Structural Biology

    

Canu

Homepage

Install with bioconda

Third generation
sequencing

    

Circlator

Homepage

Install with bioconda

Third generation
sequencing

    

DALIGNER

Homepage

Install with bioconda

Third generation
sequencing

    

DBG2OLC

Homepage

Install with bioconda

Third generation
sequencing

    

Flye

Homepage

Install with bioconda

Third generation
sequencing

    

MHAP

Homepage

Install with bioconda

Third generation
sequencing

    

Miniasm

Homepage

Install with bioconda

Third generation
sequencing

    

Raven

Homepage

Install with bioconda

Third generation
sequencing

    

SMARTdenovo

Homepage

Install with bioconda

Third generation
sequencing

    

SPAdes

Homepage

Install with bioconda

Third generation
sequencing

    

Wtdbg2

Homepage

Install with bioconda

Third generation
sequencing

    

Cromwell

Homepage

Install with bioconda

Workflow manager

    

Nextflow

Homepage

Install with bioconda

Workflow manager

    

Snakemake

Homepage

Install with bioconda

Workflow manager

    
Engineering Sciences
Name Links  Category Restricted License GPU Acceleration
OpenFOAM Homepage CAE, CFD and Engineering     
ABINIT  Homepage Chemistry    
Atomic Simulation Environment  Homepage Chemistry    
CP2K Homepage Chemistry    
GPAW Homepage Chemistry    
Libxc Homepage Chemistry    
NWChem Homepage Chemistry    
Psi4 Homepage Chemistry    
Q-Chem Homepage Chemistry End users require valid unlimited-core license  
WRF Homepage Geosciences     
GROMACS Homepage Molecular Dynamics    
LAMMPS Homepage Molecular Dynamics    
NAMD Homepage Molecular Dynamics Non-
commercial
use		  

Libraries
Name Links  Category Restricted License GPU Acceleration
oneDNN Homepage AI, Machine and Deep Learning    
Boost Homepage Data and I/O    
HDF5 Homepage Data and I/O    
NetCDF Homepage Data and I/O    
NetCDF Fortran  Homepage Data and I/O    
Parallel HDF5  Homepage Data and I/O    
Armadillo  Homepage Math and Numerical Libraries     
ARPACK-NG  Homepage Math and Numerical Libraries     
FFTW Homepage Math and Numerical Libraries     
GNU Scientific Library  Homepage Math and Numerical Libraries     
Intel MKL Homepage Math and Numerical Libraries  Available to end users via. A*CRC site license  
METIS Homepage Math and Numerical Libraries     
PLASMA Homepage Math and Numerical Libraries     
qrupdate Homepage Math and Numerical Libraries     
SCOTCH Homepage Math and Numerical Libraries     
SuiteSparse  Homepage Math and Numerical Libraries     
Intel MPI Homepage MPI Libraries Available to end users via. A*CRC site license  
mpi4py Homepage MPI Libraries    
MVAPICH2 Homepage MPI Libraries    
OpenMPI Homepage MPI Libraries    
SGI MPT and SHMEM  Homepage MPI Libraries Closed source, for use on Stratus HPC system.  

Compilers and Languages

Name

Links

Category

Restricted
License

GPU
Acceleration

GNU Compiler
Collection 

Homepage 

 

 

Compilers

    

Intel Compilers 

Homepage 

Compilers

Available to end
users via 
A*CRC site license

  

Intel SPMD
Program Compiler 

Homepage 

Compilers

    

GNU Octave 

Homepage 

Scientific / Programming
Languages

    

Intel Distribution
for Python

Homepage 

Scientific / Programming
Languages

    

Python

Homepage

Scientific / Programming
Languages

    

R

Homepage

Scientific / Programming
Languages

    

Tools

Name

Links

Category

Restricted
License 

GPU
Acceleration 

CMake

Homepage

Development Tools 

    

EasyBuild

Homepage 

Development Tools 

    

GNU
Autotools

Homepage 

Development Tools 

    

Intel Parallel
Studio XE 

Homepage 

Development Tools 

Available to end
users via A*CRC
site license

  

ImageMagick

Homepage 

Graphics and
Visualisation 

    

ParaView

Homepage 

 

 

 

Graphics and
Visualisation 

    

PAPI

Homepage 

Performance Tools

    

SGI MPI
PerfBoost 

Homepage 

Performance Tools

Closed source,
for use on
Stratus HPC
system.

  

SGI MPI
Perfcatcher 

Homepage 

Performance Tools

Closed source,
for use on
Stratus HPC
system.

  

Valgrind

Homepage 

Performance Tools

    

hwloc

Homepage 

System Tools

    

Singularity

Homepage 

System Tools