Biosciences, Bioinformatics and Biomedicine

Name

Links

Category

Restricted License

GPU Acceleration

Abyss




High-Throughput
Sequencing

  

Adam




High-Throughput
Sequencing

  

Bowtie2




High-Throughput
Sequencing

  

Burrow-Wheeler
Aligner




High-Throughput
Sequencing

  

Delly




High-Throughput
Sequencing

  

Fastp




High-Throughput
Sequencing

  

GATK3




High-Throughput
Sequencing

  

GATK4




High-Throughput
Sequencing

  

Pear




High-Throughput
Sequencing

  

Sambamba




High-Throughput
Sequencing

  

Selscan




High-Throughput
Sequencing

  

Beagle-lib




Linkage/
Phylogenetics

  

RAxML




Linkage/
Phylogenetics

  

Maxquant




Mass Spectrometry

Maxquant Freeware Software License

 

Autodock-vina




Molecular Docking

  

Blast




Sequence Analysis

  

Diamond




Sequence Analysis

  

Magicblast




Sequence Analysis

  

Meme




Sequence Analysis

  

rDock




Structural Biology

  

Canu




Third generation
sequencing

  

Circlator




Third generation
sequencing

  

DALIGNER




Third generation
sequencing

  

DBG2OLC




Third generation
sequencing

  

Flye




Third generation
sequencing

  

MHAP




Third generation
sequencing

  

Miniasm




Third generation
sequencing

  

Raven




Third generation
sequencing

  

SMARTdenovo




Third generation
sequencing

  

SPAdes




Third generation
sequencing

  

Wtdbg2




Third generation
sequencing

  

Cromwell




Workflow manager

  

Nextflow




Workflow manager

  

Snakemake




Workflow manager

  

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

Libraries

NameLinks CategoryRestricted LicenseGPU Acceleration
oneDNNHomepage
AI, Machine and Deep Learning  
BoostData and I/O  
HDF5Data and I/O  
NetCDFData and I/O  
NetCDF Fortran Data and I/O  
Parallel HDF5 Data and I/O  
Armadillo Math and Numerical Libraries   
ARPACK-NG Math and Numerical Libraries   
FFTWMath and Numerical Libraries   
GNU Scientific Library Math and Numerical Libraries   
Intel MKLMath and Numerical Libraries Available to end users via. A*CRC site license 
METISMath and Numerical Libraries   
PLASMAMath and Numerical Libraries   
qrupdateMath and Numerical Libraries   
SCOTCHMath and Numerical Libraries   
SuiteSparse Math and Numerical Libraries   
Intel MPIMPI LibrariesAvailable to end users via. A*CRC site license 
mpi4pyMPI Libraries  
MVAPICH2MPI Libraries  
OpenMPIMPI Libraries  
SGI MPT and SHMEM MPI LibrariesClosed source, for use on Stratus HPC system. 

Compilers and Languages

Name

Links

Category

Restricted
License

GPU
Acceleration

GNU Compiler
Collection 

 

 

 

Compilers

Intel Compilers 

 

Compilers

Available to end
users via 
A*CRC site license

Intel SPMD
Program Compiler 

 

Compilers

GNU Octave 

 

Scientific / Programming
Languages

Intel Distribution
for Python

 

Scientific / Programming
Languages

Python

Scientific / Programming
Languages

R

Scientific / Programming
Languages


Tools

Name

Links

Category

Restricted
License 

GPU
Acceleration 

CMake

Development Tools 

EasyBuild

 

Development Tools 

GNU
Autotools

 

Development Tools 

Intel Parallel
Studio XE 

 

Development Tools 

Available to end
users via A*CRC
site license

ImageMagick

 

Graphics and
Visualisation 

ParaView

 

 

 

 

Graphics and
Visualisation 

PAPI

 

Performance Tools

SGI MPI
PerfBoost 

 

Performance Tools

Closed source,
for use on
Stratus HPC
system.

SGI MPI
Perfcatcher 

 

Performance Tools

Closed source,
for use on
Stratus HPC
system.

Valgrind

 

Performance Tools

hwloc

 

System Tools

Singularity

 

System Tools


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