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Warning!

Puhti and Mahti will be decommissioned after Roihu becomes available. Users should clean up unnecessary files and move any required data by the end of August 2026. See the Roihu data preparation instructions for details.

Puhti scratch is very full: keep only active data there and move or delete everything else. No new Puhti scratch quota will be granted.

Applications

Cannot find the application you are looking for?

  • See here for ways to install software yourself .
  • You may also contact CSC Service Desk with your software installation request. Given enough requests, we may consider pre-installing a particular application, or purchasing a license for it if the software in question is proprietary.
  • Although we cannot promise to pre-install all requested applications, CSC Service Desk is happy to support you in installing software yourself.

Applications in alphabetical order

A

  • ABAQUS — Dassault Systemes' SIMULIA academic research suite
  • Accelerated visualization — A selection of GPU accelerated visualization applications
  • Alphafold — Protein 3D structure prediction
  • Amber — Molecular dynamics suite
  • AMS — Modelling suite providing the ADF engine
  • AMS-GUI — AMS integrated GUI
  • ANSYS — ANSYS Academic engineering simulation software suite
  • ArcGIS Python API — Spatial analysis and data science

B

  • BamTools — Tools for working with BAM formatted files
  • BayeScan — Tool for identifying candidate loci under natural selection based on allele frequencies in populations
  • BioPerl — Perl environment with bioperl extension
  • Biopython — Python environment with biopython and other bioinformatics related Python libraries
  • BLAST — Sequence similarity search tool for nucleotides and proteins
  • Blender — 3D modeling, visualization and rendering software
  • Bowtie2 — Short read aligner
  • BRAKER — Automatic genome annotator for eucaryots
  • BWA — Short read aligner

C

  • CD-HIT — Sequence clustering and redundancy removal tool
  • Chipster  — Easy-to-use analysis platform for RNA-seq, single cell RNA-seq and other NGS data
  • Chipster_genomes — Tool to download aligner indexes used by Chipster to Puhti
  • Cirq-on-iqm — open-source cirq adapter for quantum computing
  • CloudCompare — for visualizing, editing and processing point clouds
  • compute-sanitizer — Functional correctness checking suite included in the CUDA toolkit
  • COMSOL Multiphysics — General-purpose simulation software
  • COSMO-RS — Toolbox for predictive property calculation of liquids
  • CP2K — DFT, quantum chemistry, QM/MM, AIMD etc. in particular for periodic systems
  • cProfile — Built-in profiler for Python programs
  • CryoSPARC — Tool to analyse Cryo-EM data on Puhti/Mahti
  • CSD — Cambridge Crystallographic Database - organic and metallo-organic crystal structures and tools
  • cuda-gdb — Nvidia extension of the GNU debugger GDB
  • Cutadapt — Trimming high-throughput sequencing reads

D

  • DDT — Parallel debugger
  • Desktop — Remote desktop environment
  • Diamond — Sequence similarity search tool for proteins and nucleotides

E

  • eBay's tsv-tools  — Utilities for manipulating large tabular data files
  • Elmer — Open source multi-physics FEM package
  • EMBOSS — Toolkit for classical sequence analysis
  • Entrez Direct — Entrez direct - command line tool to search and retrieve data from NCBI
  • Exonerate — A generic tool for pairwise sequence comparison

F

  • FastQC — Quality control tool for high throughput sequence data
  • Finnish Tagtools  — Finnish Tagtools
  • finnish-parse  — Dependency Parser for Finnish
  • FORCE — for mass-processing of medium-resolution satellite images
  • Freebayes — Genetic variant detector

G

  • Gaussian — Versatile computational chemistry package
  • GDAL — for geospatial data formats
  • gdb — GNU debugger for compiled programs
  • Geoconda — Python libraries for spatial analysis
  • GOLD — Protein Ligand Docking Software
  • GPAW — Versatile DFT package
  • Grace — Plotting tool for xvg-files in particular
  • GRASS GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
  • GROMACS — Fast and versatile classical molecular dynamics

H

  • HADDOCK3 — High Ambiguity Driven biomolecular DOCKing
  • HFST  — Helsinki Finite-State Transducer Technology
  • HFST-fi  — Helsinki Finite-State Technology for Finnish
  • HFST-sv  — Helsinki Finite-State Technology for Swedish
  • HMMER — Toolkit to create and use sequence profile hidden Markov models
  • HUMAnN — Profiling microbial pathways with metagenomic data
  • HyperQueue — Scheduler for sub-node tasks

I

  • IDL — Programming Language, Numeric Analysis, Manipulation and Visualization of Scientific Data
  • Illumina BaseSpace — Command line client for retrieving data from the Illumina BaseSpace environment
  • Intel Trace Analyzer and Collector (ITAC) — MPI profiling and tracing tool
  • Intel VTune Profiler — Performance analysis tool for single core and threading performance
  • InterProScan — Protein signature/motif search tool
  • iPyrad — toolkit for population genetic and phylogenetic studies of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS)

J

  • JAX — Autograd and XLA, brought together for high-performance machine learning
  • Julia Language — High-level, high-performance dynamic programming language for numerical computing
  • Julia-Jupyter — Interactive computational environment for Julia
  • Jupyter — Interactive computational environment for Python
  • Jupyter for courses — A version of the Jupyter app for course environments

K

  • Kaldi  — Kaldi Speech Recognition Toolkit
  • Kraken — Taxonomic sequence classification system
  • Krona visualization tool — Visualization tool for taxonomic classification and other hierarchical data

L

  • LAMMPS — Fast molecular dynamics engine with large force field selection
  • LAStools — for LiDAR datasets
  • Lazypipe — A stand-alone pipeline for identifying viruses in host-associated or environmental samples

M

  • MACS2/3 — ChIP-Seq analysis tool
  • Maestro — Versatile drug discovery and materials modeling suite
  • MATLAB — High-level technical computing language
  • MaxQuant  — A proteomics software for processing of Mass-spectromtery data
  • Megahit — Metagenomics assembly
  • MetaPhlAn — Profiling the composition of microbial communities with metagenomic data
  • Minimap2 — Short read aligner
  • MIRA — Whole genome shotgun and EST sequence Assembler
  • Molden — Processing program for molecular and electronic structure calculations
  • MOLPRO — Package for accurate ab initio quantum chemistry calculations
  • Mothur — Package for microbial community analysis of amplicon sequencing data
  • MrBayes — Program for inferring phylogenies using Bayesian methods

N

  • NAMD — Highly scalable classical molecular dynamics
  • NASA Ames Stereo Pipeline (ASP) — for processing stereo images
  • ncu — Nvidia CUDA kernel profiler
  • Nextflow — Nextflow is a scientific workflow management system for creating scalable, portable, and reproducible workflows
  • NMRLipids — NMRLipids databank containing MD simulations
  • nsys — Nvidia GPU and CPU profiler
  • nvprof — Nvidia profiling tool that collects and views profiling data
  • NWChem — A computational chemistry software package designed to perform well on parallel HPC systems

O

P

  • PALM — Meteorological model system for atmospheric and oceanic boundary-layer flows
  • PANNZER2/SANSPANZ — Automatic protein annotation tool
  • ParaView — Free open-source visualization application
  • PCL — for 2D/3D image and point cloud processing
  • PDAL — for point cloud translations and processing
  • pdb — Built-in Python debugger
  • Pennylane — Free open-source software framework for quantum machine learning and quantum computing
  • perf — Command line tool for performance analysis
  • Picard Tools — Tools for working with SAM,BAM,CRAM and VCF files
  • PLUMED — Library and tools for enhanced sampling methods
  • Prokka — Rapid prokaryotic genome annotation
  • Python — The programming language and its modules at CSC
  • Python Data — Collection of Python libraries for data analytics and machine learning
  • PyTorch — Machine learning framework for Python

Q

  • QGIS — General purpose GIS software family for viewing, editing and analysing geospatial data
  • QIIME — Package for microbial community analysis of amplicon sequencing data
  • Qiskit — open-source toolkit for useful quantum computing
  • Qiskit-on-iqm — open-source qiskit adapter for quantum computing
  • Quantum ESPRESSO — Electronic-structure calculations and materials modeling at the nanoscale

R

  • R for GIS — R spatial analysis libraries
  • r-env — R and RStudio Server
  • RAPIDS — Suite of libraries for data analytics and machine learning on GPUs
  • RAxML — Program for inferring phylogenies with likelihood
  • Roary — Pan genome pipeline
  • RStudio IDE — Integrated development environment for R

S

  • SAGA GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
  • SageMath — Free open-source mathematics software system
  • SALMON — Program to produce transcript-level quantification estimates from RNA-seq data
  • SAMtools — Utilities for managing SAM/BAM formatted alignment files
  • Scalasca — Performance profiler for parallel programs
  • Seismic Unix — for processing of 2D seismic or GPR data sets.
  • Sen2Cor — for atmospheric-, terrain and cirrus correction of the Sentinel-2 products
  • Sen2mosaic — for download, preprocessing and mosaicing of Sentinel-2 products
  • Seqtk — Tool for processing sequences in the FASTA or FASTQ format
  • Snakemake — Snakemake is a scientific workflow management system for creating scalable, portable, and reproducible workflows
  • SNAP — for remote sensing applications
  • SOFI3D — for 3D finite-difference seismic wave simulation
  • SPAdes — Genome assembly
  • Spark — High-performance distributed computing framework
  • Stacks — Pipeline for building loci from short-read sequences (e.g. RAD-seq data)
  • STAR — Short read aligner
  • Star-CCM+ — Computational Fluid Dynamics software by Siemens Digital Industries Software
  • Structure — Inference of population structure in genetics

T

  • TensorBoard — The visualization toolkit for TensorFlow
  • TensorFlow — Deep learning library for Python
  • TmoleX — GUI for setting up and analyzing TURBOMOLE jobs
  • TopHat — Splice junction mapper for RNA-Seq reads
  • Trimmomatic — Trim Illumina paired-end and single-read data
  • Trinity — Transcriptome assembly tool
  • TURBOMOLE — Efficient program package for electronic structure calculations

U

  • UDPipe  — UDPipe Kielipankki version

V

  • VASP — Ab initio DFT electronic structures
  • Velvet — Genome assembler
  • VirusDetect — Virus identification with sRNA data
  • VisIt — Free open-source visualization application
  • Visual Studio Code — Source code editor
  • VMD — Molecular visualization program

W

  • Whisper — General-purpose speech recognition model
  • WhiteboxTools — an advanced geospatial data analysis platform
  • wtdbg2 — Fast assembler for long-read data

X

Z

  • Zonation — Spatial conservation prioritization framework