Applications by availability

Applications available on

• Roihu — New national CSC supercomputer replacing Puhti and Mahti
• Mahti — CSC supercomputer for massively parallel jobs
• Puhti — CSC supercomputer for small and medium jobs
• LUMI — EuroHPC supercomputer for CPU and especially GPU jobs

Interactive web applications available on

• Roihu web interface
• Mahti web interface
• Puhti web interface
• LUMI web interface

Roihu

• Abaqus — Dassault Systemes' SIMULIA academic research suite
• ABySS — De novo, parallel, paired-end sequence assembler
• AdmixTools — Inference of population admixture from f-statistics
• ADMIXTURE — Maximum-likelihood estimation of individual ancestries from SNP data
• Amber — Molecular dynamics suite
• AMS — Modelling suite providing the ADF engine
• AMS-GUI — AMS integrated GUI
• ANGSD — Analysis of next-generation sequencing data via genotype likelihoods
• Ansys — Ansys Academic research CFD
• antiSMASH — Detection of secondary-metabolite biosynthesis gene clusters in microbial genomes
• ASTRAL — Coalescent-based species-tree estimation from gene trees
• AUGUSTUS — Gene prediction in eukaryotic genomic sequences
• BamTools — Tools for working with BAM formatted files
• Barrnap — Rapid ribosomal RNA (rRNA) prediction
• BBMap — BBTools short-read aligner and sequence-processing suite
• BCFtools — Variant calling and VCF/BCF manipulation
• BEDOPS — Set operations on genomic intervals (BED)
• BEDTools — Genome arithmetic on BED/VCF/GFF intervals
• Bio-apps — Access module to a collection of applications and software often used in biosciences
• BioPerl — Perl environment with bioperl extension
• BLAST — Sequence similarity search tool for nucleotides and proteins
• Blender — 3D modeling, visualization and rendering software
• Bowtie — Ultrafast, memory-efficient short read aligner
• Bowtie2 — Short read aligner
• Bracken — Species abundance estimation from Kraken2 output
• BRAKER — Automatic genome annotation pipeline for eukaryotes
• BUSCO — Genome/transcriptome completeness assessment via orthologs
• BWA — Short read aligner
• bwa-mem2 — Faster successor to bwa mem
• Canu — Long-read (PacBio/Nanopore) genome assembler
• CD-HIT — Sequence clustering and redundancy removal tool
• CDO — Command line tools to manipulate and analyse Climate and NWP model Data
• CheckM2 — Genome quality assessment via machine learning
• CloudCompare — for visualizing, editing and processing point clouds
• CLUMPP — Alignment of replicate cluster assignments from population-structure analyses
• Clustal Omega — Multiple sequence alignment
• ClustalW — Multiple sequence alignment
• compute-sanitizer — Functional correctness checking suite included in the CUDA toolkit
• COMSOL Multiphysics — General-purpose simulation software
• COSMO-RS — Toolbox for the prediction of fluid phase thermodynamic properties using the COSMO-RS model
• CP2K — DFT, quantum chemistry, QM/MM, AIMD etc. in particular for periodic systems
• cuda-gdb — Nvidia extension of the GNU debugger GDB
• Cufflinks — Transcript assembly and differential expression for RNA-Seq
• deepTools — Tools for exploring deep-sequencing coverage data
• Diamond — Sequence similarity search tool for proteins and nucleotides
• Dorado — GPU-accelerated Oxford Nanopore basecaller
• eBay's tsv-utils — Utilities for manipulating large tabular data files
• eggNOG-mapper — Functional annotation of sequences via orthology (eggNOG)
• Elmer — Open source multi-physics FEM package
• EMBOSS — Toolkit for classical sequence analysis
• Exonerate — A generic tool for pairwise sequence comparison
• fastp — Fast all-in-one FASTQ preprocessing and QC
• FastQC — Quality control tool for high throughput sequence data
• FASTX-Toolkit — FASTA/FASTQ short-read preprocessing tools
• FFmpeg — Tools and libraries for recording, converting and streaming audio and video
• Freebayes — Genetic variant detector
• gapseq — Genome-scale metabolic network reconstruction and analysis
• GATK — Genome Analysis Toolkit for variant discovery
• Gaussian — Versatile computational chemistry package
• GDAL — for geospatial data formats
• gdb — GNU debugger for compiled programs
• GetOrganelle — Assembly of organelle genomes from whole-genome sequencing data
• GPAW — Versatile DFT package
• GRASS GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• GROMACS — Fast and versatile classical molecular dynamics
• GTDB-Tk — Taxonomic classification of bacterial and archaeal genomes using the GTDB
• HeLI-OTS — Off-the-shelf language identifier with language models for 220 languages
• HISAT2 — Spliced aligner for RNA-seq and DNA reads
• HMMER — Toolkit to create and use sequence profile hidden Markov models
• HUMAnN — Profiling microbial pathways with metagenomic data
• HybPiper — Target-capture (Hyb-Seq) locus recovery for phylogenomics
• HyperQueue — Scheduler for sub-node tasks
• HyPhy — Hypothesis testing on phylogenies (selection analysis)
• IGV — Integrative Genomics Viewer - interactive genome browser
• inStrain — Strain-level population genomics from metagenomic mappings
• iPyrad — toolkit for population genetic and phylogenetic studies of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS)
• IQ-TREE — Maximum-likelihood phylogenetic inference
• JAX — Autograd and XLA, brought together for high-performance machine learning
• Jellyfish — Fast k-mer counting
• Julia Language — High-level, high-performance dynamic programming language for numerical computing
• kp-spell (enchant) — Finnish and Swedish spell-checking via the enchant interface
• Kraken — Taxonomic sequence classification system
• LAMMPS — Fast molecular dynamics engine with large force field selection
• LAStools — for LiDAR datasets
• Maestro — Versatile drug discovery and materials modeling suite
• MAFFT — Multiple sequence alignment
• Mash — Fast genome/metagenome distance estimation (MinHash)
• MATLAB — High-level technical computing language
• medaka — Nanopore consensus and variant calling
• Megahit — Metagenomics assembly
• MEME Suite — Motif discovery and analysis (MEME Suite)
• MetaBAT — Metagenome binning (MetaBAT2)
• MetaHipMer2 — GPU-accelerated metagenome assembly
• MetaPhlAn — Profiling the composition of microbial communities with metagenomic data
• MICOM — Metabolic modelling of microbial communities
• minibwa — Short-read aligner, successor to BWA-MEM
• Minimap2 — Short read aligner
• MMseqs2 — Very fast protein search and clustering
• 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
• MUMmer — Genome alignment (MUMmer)
• MUSCLE — Multiple sequence alignment (v3)
• MUSCLE5 — Multiple sequence alignment (v5)
• NAMD — Highly scalable classical molecular dynamics
• NCBI C++ Toolkit — NCBI C++ Toolkit libraries and command-line applications
• ncu — Nvidia CUDA kernel profiler
• Nextflow — Nextflow is a scientific workflow management system for creating scalable, portable, and reproducible workflows
• nsys — Nvidia GPU and CPU profiler
• OpenDroneMap (ODM) — for processing aerial drone imagery
• OpenFOAM — OpenFOAM® is the leading free, open source software for computational fluid dynamics (CFD)
• openSMILE — Toolkit for extracting audio features for speech and music analysis
• ORCA — General-purpose quantum chemistry package
• Orfeo ToolBox — for remote sensing applications
• ParaView — Free open-source visualization application
• PDAL — for point cloud translations and processing
• pdb — Built-in Python debugger
• PHYLIP — PHYLIP phylogeny inference package
• Picard Tools — Tools for working with SAM,BAM,CRAM and VCF files
• Praat — Toolkit for annotating, processing and analysing speech and other audio samples
• Prodigal — Prokaryotic gene prediction
• Python — The programming language and its modules at CSC
• Python Data — Collection of Python libraries for data analytics and machine learning
• Python-geo — Python libraries for spatial analysis
• PyTorch — Machine learning framework for Python
• QGIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• R for GIS — R spatial analysis libraries
• r-env — R and RStudio Server
• RAxML — Program for inferring phylogenies with likelihood
• RAxML-NG — Maximum-likelihood phylogenetic inference (RAxML-NG)
• Roary — Pan genome pipeline
• run_dbcan — Automated carbohydrate-active enzyme (CAZyme) annotation
• SAGA GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• SameStr — Strain-level sharing analysis from metagenomic SNV profiles
• SAMtools — Utilities for managing SAM/BAM formatted alignment files
• SeqKit — Cross-platform FASTA/FASTQ toolkit
• 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
• SortMeRNA — Filtering and sorting of rRNA reads from (meta)transcriptomic data
• SPAdes — Genome assembly
• SRA Toolkit — NCBI SRA Toolkit for accessing and converting SRA data
• STAR — Short read aligner
• Star-CCM+ — Computational Fluid Dynamics software by Siemens Digital Industries Software
• SteadierCom — Steady-state metabolic simulation of microbial communities
• StrAuto — Automation and parallelization of STRUCTURE analysis
• StringTie — Transcript assembly and quantification for RNA-Seq
• Structure — Inference of population structure in genetics
• Structure Harvester — Post-processing of STRUCTURE results (Evanno method)
• TensorFlow — Deep learning library for Python
• TopHat — Splice junction mapper for RNA-Seq reads
• trankit — Transformer-based Python toolkit for multilingual Natural Language Processing (NLP)
• Trimmomatic — Trim Illumina paired-end and single-read data
• TURBOMOLE — Fast and robust quantum chemistry program package
• UDPipe — Trainable pipeline for tokenization, tagging, lemmatization and dependency parsing
• VASP — Ab initio DFT electronic structures
• VCFtools — VCF manipulation and statistics
• VisIt — Free open-source visualization application
• vLLM — A fast and easy-to-use library for LLM inference and serving
• VMD — Molecular visualization program
• vrt-tools — Tools for converting VRT (Vertical Text) corpus files
• VSEARCH — Versatile sequence search and clustering
• WhiteboxTools — an advanced geospatial data analysis platform
• Zonation — Spatial conservation prioritization framework

Mahti

• Alphafold — Protein 3D structure prediction
• AMS — Modelling suite providing the ADF engine
• compute-sanitizer — Functional correctness checking suite included in the CUDA toolkit
• 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
• cuda-gdb — Nvidia extension of the GNU debugger GDB
• DDT — Parallel debugger
• Elmer — Open source multi-physics FEM package
• FireWorks — FireWorks is a free, open-source tool for defining, managing and executing workflows with multiple steps and complex dependencies
• Gaussian — Versatile computational chemistry package
• GDAL — for geospatial data formats
• gdb — GNU debugger for compiled programs
• Geoconda — Python libraries for spatial analysis
• GPAW — Versatile DFT package
• GROMACS — Fast and versatile classical molecular dynamics
• IDL — Programming Language, Numeric Analysis, Manipulation and Visualization of Scientific Data
• JAX — Autograd and XLA, brought together for high-performance machine learning
• Julia Language — High-level, high-performance dynamic programming language for numerical computing
• LAMMPS — Fast molecular dynamics engine with large force field selection
• MATLAB — High-level technical computing language
• Molden — Processing program for molecular and electronic structure calculations
• MOLPRO — Package for accurate ab initio quantum chemistry calculations
• NAMD — Highly scalable classical molecular dynamics
• ncu — Nvidia CUDA kernel profiler
• 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
• Open Babel — Program to interconvert file formats currently used in molecular modeling
• OpenFOAM — OpenFOAM® is the leading free, open source software for computational fluid dynamics (CFD)
• ORCA — General-purpose quantum chemistry package
• PALM — Meteorological model system for atmospheric and oceanic boundary-layer flows
• ParaView — Free open-source visualization application
• PDAL — for point cloud translations and processing
• pdb — Built-in Python debugger
• perf — Command line tool for performance analysis
• PLUMED — Library and tools for enhanced sampling methods
• Qiskit — open-source toolkit for useful quantum computing
• Quantum ESPRESSO — Electronic-structure calculations and materials modeling at the nanoscale
• r-env — R and RStudio Server
• Scalasca — Performance profiler for parallel programs
• Star-CCM+ — Computational Fluid Dynamics software by Siemens Digital Industries Software
• TURBOMOLE — Fast and robust quantum chemistry program package
• VisIt — Free open-source visualization application

Puhti

• Alphafold — Protein 3D structure prediction
• AMS — Modelling suite providing the ADF engine
• ArcGIS Python API — Spatial analysis and data science
• BayeScan — Tool for identifying candidate loci under natural selection based on allele frequencies in populations
• Biopython — Python environment with biopython and other bioinformatics related Python libraries
• Blender — 3D modeling, visualization and rendering software
• Chipster_genomes — Tool to download aligner indexes used by Chipster to Puhti
• compute-sanitizer — Functional correctness checking suite included in the CUDA toolkit
• 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
• DDT — Parallel debugger
• eBay's tsv-utils — Utilities for manipulating large tabular data files
• Elmer — Open source multi-physics FEM package
• Entrez Direct — Entrez direct - command line tool to search and retrieve data from NCBI
• FFmpeg — Tools and libraries for recording, converting and streaming audio and video
• FireWorks — FireWorks is a free, open-source tool for defining, managing and executing workflows with multiple steps and complex dependencies
• Gaussian — Versatile computational chemistry package
• gdb — GNU debugger for compiled programs
• GOLD — Protein Ligand Docking Software
• GPAW — Versatile DFT package
• Grace — Plotting tool for xvg-files in particular
• GROMACS — Fast and versatile classical molecular dynamics
• HeLI-OTS — Off-the-shelf language identifier with language models for 220 languages
• 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
• JAX — Autograd and XLA, brought together for high-performance machine learning
• kp-spell (enchant) — Finnish and Swedish spell-checking via the enchant interface
• Krona visualization tool — Visualization tool for taxonomic classification and other hierarchical data
• LAMMPS — Fast molecular dynamics engine with large force field selection
• Lazypipe — A stand-alone pipeline for identifying viruses in host-associated or environmental samples
• MACS2/3 — ChIP-Seq analysis tool
• 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
• NAMD — Highly scalable classical molecular dynamics
• ncu — Nvidia CUDA kernel profiler
• 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
• Octave — High-level interpreted language for numerical computations
• Open Babel — Program to interconvert file formats currently used in molecular modeling
• openSMILE — Toolkit for extracting audio features for speech and music analysis
• ORCA — General-purpose quantum chemistry package
• PALM — Meteorological model system for atmospheric and oceanic boundary-layer flows
• PANNZER2/SANSPANZ — Automatic protein annotation tool
• ParaView — Free open-source visualization application
• pdb — Built-in Python debugger
• perf — Command line tool for performance analysis
• PLUMED — Library and tools for enhanced sampling methods
• Praat — Toolkit for annotating, processing and analysing speech and other audio samples
• Prokka — Rapid prokaryotic genome annotation
• QIIME — Package for microbial community analysis of amplicon sequencing data
• Qiskit — open-source toolkit for useful quantum computing
• Quantum ESPRESSO — Electronic-structure calculations and materials modeling at the nanoscale
• RStudio IDE — Integrated development environment for R
• SageMath — Free open-source mathematics software system
• SALMON — Program to produce transcript-level quantification estimates from RNA-seq data
• Scalasca — Performance profiler for parallel programs
• Stacks — Pipeline for building loci from short-read sequences (e.g. RAD-seq data)
• TmoleX — GUI for setting up and analyzing TURBOMOLE jobs
• trankit — Transformer-based Python toolkit for multilingual Natural Language Processing (NLP)
• Trinity — Transcriptome assembly tool
• TURBOMOLE — Fast and robust quantum chemistry program package
• UDPipe — Trainable pipeline for tokenization, tagging, lemmatization and dependency parsing
• Velvet — Genome assembler
• VirusDetect — Virus identification with sRNA data
• VisIt — Free open-source visualization application
• vrt-tools — Tools for converting VRT (Vertical Text) corpus files
• Whisper — General-purpose speech recognition model
• wtdbg2 — Fast assembler for long-read data
• XHMM (eXome-Hidden Markov Model) — Copy number variation calling from targeted sequencing data

LUMI

• Accelerated visualization — A selection of GPU accelerated visualization applications
• Amber — Molecular dynamics suite
• Blender — 3D modeling, visualization and rendering software
• Cirq-on-iqm — open-source cirq adapter for quantum computing
• CP2K — DFT, quantum chemistry, QM/MM, AIMD etc. in particular for periodic systems
• Desktop — Remote desktop environment
• Elmer — Open source multi-physics FEM package
• GDAL — for geospatial data formats
• Geoconda — Python libraries for spatial analysis
• GRASS GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• GROMACS — Fast and versatile classical molecular dynamics
• HADDOCK3 — High Ambiguity Driven biomolecular DOCKing
• HyperQueue — Scheduler for sub-node tasks
• 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
• LAMMPS — Fast molecular dynamics engine with large force field selection
• Maestro — Versatile drug discovery and materials modeling suite
• MATLAB — High-level technical computing language
• NAMD — Highly scalable classical molecular dynamics
• Nextflow — Nextflow is a scientific workflow management system for creating scalable, portable, and reproducible workflows
• NMRLipids — NMRLipids databank containing MD simulations
• OpenFOAM — OpenFOAM® is the leading free, open source software for computational fluid dynamics (CFD)
• PALM — Meteorological model system for atmospheric and oceanic boundary-layer flows
• ParaView — Free open-source visualization application
• PDAL — for point cloud translations and processing
• Pennylane — Free open-source software framework for quantum machine learning and quantum computing
• perf — Command line tool for performance analysis
• PLUMED — Library and tools for enhanced sampling methods
• QGIS — General purpose GIS software family for viewing, editing and analysing geospatial 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
• SAGA GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• Star-CCM+ — Computational Fluid Dynamics software by Siemens Digital Industries Software
• TensorBoard — The visualization toolkit for TensorFlow
• TensorFlow — Deep learning library for Python
• VisIt — Free open-source visualization application
• Visual Studio Code — Source code editor
• WhiteboxTools — an advanced geospatial data analysis platform

Roihu web interface

• Blender — 3D modeling, visualization and rendering software
• CloudCompare — for visualizing, editing and processing point clouds
• COMSOL Multiphysics — General-purpose simulation software
• Desktop — Remote desktop environment
• GRASS GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• Jupyter — Interactive computational environment for Python
• MATLAB — High-level technical computing language
• ParaView — Free open-source visualization application
• QGIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• SAGA GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• SNAP — for remote sensing applications
• VisIt — Free open-source visualization application
• VMD — Molecular visualization program
• Zonation — Spatial conservation prioritization framework

Mahti web interface

• CryoSPARC — Tool to analyse Cryo-EM data on Puhti/Mahti
• Desktop — Remote desktop environment
• 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
• MATLAB — High-level technical computing language
• TensorBoard — The visualization toolkit for TensorFlow
• Visual Studio Code — Source code editor

Puhti web interface

• Accelerated visualization — A selection of GPU accelerated visualization applications
• Blender — 3D modeling, visualization and rendering software
• CryoSPARC — Tool to analyse Cryo-EM data on Puhti/Mahti
• Desktop — Remote desktop environment
• Grace — Plotting tool for xvg-files in particular
• 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
• ParaView — Free open-source visualization application
• RStudio IDE — Integrated development environment for R
• TensorBoard — The visualization toolkit for TensorFlow
• VisIt — Free open-source visualization application
• Visual Studio Code — Source code editor

LUMI web interface

• Accelerated visualization — A selection of GPU accelerated visualization applications
• Blender — 3D modeling, visualization and rendering software
• Desktop — Remote desktop environment
• GRASS GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• Julia-Jupyter — Interactive computational environment for Julia
• Jupyter — Interactive computational environment for Python
• MATLAB — High-level technical computing language
• ParaView — Free open-source visualization application
• QGIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• SAGA GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• TensorBoard — The visualization toolkit for TensorFlow
• VisIt — Free open-source visualization application
• Visual Studio Code — Source code editor

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