ACCESS Resource Provider Software Discovery

intel-mpi v2021.10.0

Module: intel-mpi/2021.10.0

intel-compiler-rt32 v2023.2.1

Module: intel-compiler-rt32/2023.2.1

hisat2 v 2.2.1

Module: hisat2/ 2.2.1

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.

Domain: Biological Sciences

intel-advisor v2023.2.0

Module: intel-advisor/2023.2.0

Siesta v 5.0.0

Module: Siesta/ 5.0.0

Siesta is a computational package for performing efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

Domain: Materials Sciences

Keywords: DFT ab initio pseudopotential O(N)

Abinit v 10.4.7

Module: Abinit/ 10.4.7

Ab initio molecular dynamics.

Domain: Materials Sciences

Keywords: molecular dynamics density functional theory

Abinit v 9.4.2

Module: Abinit/ 9.4.2

Ab initio molecular dynamics.

Domain: Materials Sciences

Keywords: molecular dynamics density functional theory

phylip-suite v 3.697

Module: phylip-suite/ 3.697

PHYLIP is a free package of programs for inferring phylogenies.

Domain: Biological Sciences

Keywords: singularity bioinformatics

VASP v 6.5.1

Module: VASP/ 6.5.1

The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. VASP is not public domain software, and PSC does not provide public access to it. You must have your own VASP license in order to use it on Bridges-2. To use VASP on Bridges-2, submit the VASP request form, verifying your license information. Once you have submitted the VASP request form and your

Domain: Materials Sciences

Keywords: DFT ab initio pseudopotential

VASP v 5.4.4+VTST

Module: VASP/ 5.4.4+VTST

The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. VASP is not public domain software, and PSC does not provide public access to it. You must have your own VASP license in order to use it on Bridges-2. To use VASP on Bridges-2, submit the VASP request form, verifying your license information. Once you have submitted the VASP request form and your

Domain: Materials Sciences

Keywords: DFT ab initio pseudopotential

phdf5 v1.10.7

Module: phdf5/1.10.7

HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.

Domain: I/O libraries

Keywords: HDF hdf5 data file format

hashdeep v 4.4

Module: hashdeep/ 4.4

This is hashdeep, a set of cross-platform tools to compute hashes, or message digests, for any number of files while optionally recursively digging through the directory structure.

Domain: Other

openmpi v3.1.5-nvhpc21.2

Module: openmpi/3.1.5-nvhpc21.2

Purpose ------- The modulefile defines paths and environment variables for using OpenMPI 3.1.5 built with the NVidia HPC SDK 21.2 compilers.

Domain: libraries

openmpi v3.1.6

Module: openmpi/3.1.6

An open source Message Passing Interface implementation.

Domain: libraries

Keywords: OpenMPI MPI GNU

Trinity v 2.15.1

Module: Trinity/ 2.15.1

Trinity assembles transcript sequences from Illumina RNA-Seq data.

Domain: Biological Sciences

Keywords: singularity bioinformatics

trnascan-se v 2.0.7

Module: trnascan-se/ 2.0.7

tRNAscan-SE pioneers the large-scale use of covariance models to annotate tRNA genes in genomes.

Domain: Biological Sciences

Keywords: singularity bioinformatics

cuda v9.2.88

Module: cuda/9.2.88

CUDA is a parallel computing platform and programming model invented by NVIDIA. It enables dramatic increases in computing performance by harnessing the power of the graphics processing unit (GPU).

Domain: Libraries/GPU

FastQC v 0.11.9

Module: FastQC/ 0.11.9

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines.

Domain: Biological Sciences

Keywords: singularity bioinformatics

pilon v 1.24

Module: pilon/ 1.24

Pilon is an automated genome assembly improvement and variant detection tool.

Domain: Biological Sciences

SPAdes v 3.14.1

Module: SPAdes/ 3.14.1

SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines.

Domain: Biological Sciences

Keywords: singularity bioinformatics

GATK v 4.1.9.0

Module: GATK/ 4.1.9.0

The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data.

Domain: Biological Sciences

Keywords: singularity bioinformatics

htslib v 1.13

Module: htslib/ 1.13

HTSlib A C library for reading/writing high-throughput sequencing data.

Domain: Biological Sciences

Keywords: singularity bioinformatics

ansys v251

Module: ansys/251

The ansys installation includes ANSYS multiphysics components. Paths to ANSYS mechanical, Fluent, CFX and AutoDyn packages are added to the user path setting. The software is distributed by ANSYS, Inc: http://ansys.com

Domain: Engineering

RAxML v 8.2.9

Module: RAxML/ 8.2.9

RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It can also be used for postanalyses of sets of phylogenetic trees, analyses of alignments and, evolutionary placement of short reads

Domain: Biological Sciences

Keywords: singularity bioinformatics

TIGER v 5.32.1

Module: TIGER/ 5.32.1

Target / Integrative Genetic Element Retriever: precisely maps IGEs (a defined type of genomic island) in bacterial and archaeal genomes.

Domain: Biological Sciences

Keywords: singularity bioinformatics