libwebp (library to encode and decode images in WebP format) version 1.2.0 installed on all systems as module libwebp/1.2.0.
 

RStudio (Integrated development environment for the R language) version 1.4.1106 installed on all systems as module RStudio/1.4.1106.

snpAD (an ancient-DNA aware genotyper) version 0.3.4 installed on all systems as module snpAD/0.3.4.

Vapor (VAPOR is the Visualization and Analysis Platform for Ocean\, Atmosphere\, and Solar Researchers. VAPOR provides an interactive 3D visualization environment that can also produce animations and still frame images.) version 3.3.0 installed on all systems as module Vapor/3.3.0.

Shasta (The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.) version 0.7.0 installed on all systems as module Shasta/0.7.0.
 

FastML (tool for the reconstruction of ancestral sequences based on the phylogenetic relations between homologous sequences) version 3.11 installed on all systems as module FastML/3.11.
 

FastME (comprehensive, accurate and fast distance-based phylogeny inference program) version 2.1.6.2 installed on all systems as module FastME/2.1.6.2.

mrbayes (A program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.) version 3.2.7a installed on all systems as module mrbayes/3.2.7a. MPI version is installed on all systems as mrbayes/3.2.7a-mpi. GPU version is installed on Snowy as mrbayes/3.2.7a-gpu.

BLAST version 2.11.0+ installed on all systems as module blast/2.11.0+.
 

vmtouch (a tool for learning about and controlling the file system cache of unix and unix-like systems) version 1.3.1-20200309-4b70a9f installed on all systems as module vmtouch/1.3.1-20200309-4b70a9f.

vmtouch can be particularly helpful for managing large, randomly accessed files over networked filesystems such as crex.  See 'module help vmtouch/1.3.1-20200309-4b70a9f' for more information.

Python 3.8.7 is now installed as module python/3.8.7 and python3/3.8.7 on all systems.  The python3 module versions do not provide a 'python' name and do not conflict with python/2.x.y modules.

As usual, a number of Python packages are included with the module, including numpy, scipy, jupyter, pandas, and matplotlib.

10X Chromium Cellranger (Cell line analysis system) version 5.0.1 installed on all systems as module cellranger/5.0.1. Also installed are Cellranger single cell gene expression reference data as cellranger-data/2020-A, and Cellranger single cell V(D)J immune profiling reference data as cellranger-VDJ-data/5.0.0. These are both loaded by the new cellranger/5.0.1 module as prerequisites. For more information, see 'module help' for the newly installed modules.

kallisto (a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.) version 0.46.2 installed on all systems as module kallisto/0.46.2.
 

SACRA (SACRA splits the chimeric reads to the non-chimeric reads in PacBio long reads of MDA-treated virome sample.) version 1.0.0 installed on all systems as module SACRA/1.0.0.
 

SeqKit (A cross-platform and ultrafast toolkit for FASTA/Q file manipulation) version 0.15.0 installed on all systems as module SeqKit/0.15.0.
 

last (finds similar regions between sequences.) version 963 installed on all systems as module last/963.
 

GUSHR (Assembly-free construction of UTRs from short read RNA-Seq data on the basis of coding sequence annotation) version 1.0.0 installed on all systems as module GUSHR/1.0.0.
 

GeneMark (de novo gene prediction) version 4.62-ES is now installed as module GeneMark/4.62-es on all systems.  The key file is also updated as of today's date, 17-Jan-2021.

ProtHint (pipeline for predicting and scoring hints (in the form of introns, start and stop codons) in the genome of interest by mapping and spliced aligning predicted genes to a database of reference protein sequences) version 2.5.0 installed on all systems as module ProtHint/2.5.0.
 

Sniffles (Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore)) version 1.0.12-201218-4ff6ecb installed on all systems as module Sniffles/1.0.12-201218-4ff6ecb.
 

DelGet (finds micro- and midsize deletions (using gaps of 1-30 nt and >30 nt respectively) between orthologous regions of 3 or more species) version 5.4 installed on all systems as module DelGet/5.4.
 

Kalign (fast and accurate multiple sequence alignment algorithm) versions 1.04 and 2.04 installed on all systems as modules Kalign/1.04 and Kalign/2.04.
 

minimap2 (versatile pairwise aligner for genomic and spliced nucleotide sequences) version 2.17-r941 installed on all systems as module minimap2/2.17-r941.
 

ANGSD (software for analyzing next generation sequencing data) version 0.933 installed on all systems as module ANGSD/0.933.
 

lammps (LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel) version 29Oct2020_gcc_openmpi installed on Rackham as module lammps/29Oct2020_gcc_openmpi.
https://lammps.sandia.gov/

lp_solve (Mixed Integer Linear Programming (MILP) solver) version 5.5.2.9 installed on all systems as module lpsolve/5.5.2.9.
 

SQLite (C-language library that implements a small, fast, self-contained, high-reliability, full-featured, SQL database engine) version 3.34.0 installed on all systems as module sqlite/3.34.0.

AUGUSTUS (gene prediction) version 3.3.3 with Comparative Gene Prediction support is installed as module augustus/3.3.3-CGP on all systems.  This specific module is largely a wrapper around an EasyBuild-built module, with UPPMAX additions for copying the config directory.  See 'module help augustus/3.3.3-CGP' for more.

NeEstimator (The NeEstimator software estimates genetic effective population sizes (Ne) from genotype data.) version 2.1 installed on all systems as module NeEstimator/2.1.

RAisD (A parameter free tool to detect selective sweeps using multiple signatures and enumeration of single nucleotide polymorphism (NP) vectors. ) version 2.9 installed on all systems as module RAisD/2.9.

SNeP (Estimates trends in effective population size trajectories using genome-wide SNP data. A user can adjust parameters for sample size, mutation, phasing, and recombination rate.) version 1.1 installed on all systems as module SNeP/1.1.

IGV (high-performance, easy-to-use, interactive tool for the visual exploration of genomic data) version 2.8.13 installed on all systems as module IGV/2.8.13.  The corresponding IGVtools are available in IGVtools/2.8.13.

IGVtools (tools for preparing data for IGV display) version 2.8.13 installed on all systems as module IGVtools/2.8.13.

SHAPEIT (fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and sequencing data; version 4 is a refactored and improved version of the SHAPEIT algorithm with multiple key additional features) version v4.1.3 installed on all systems as module SHAPEIT/v4.1.3.
 

ORCA version 4.2.1 installed on all systems as module ORCA/4.2.1.

cyvcf2 version 0.30.1 installed on all systems as module cyvcf2/0.30.1.

https://github.com/brentp/cyvcf2

wrf-python (A collection of diagnostic and interpolation routines for use with output from the Weather Research and Forecasting (WRF-ARW) Model.) version 1.3.1 installed on Rackham and Snowy as module wrf-python/1.3.1.
 

IntaRNA (efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites) version 3.2.1 installed on all systems as module IntaRNA/3.2.1.
 

RNAfold, also known as ViennaRNA (a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures) version 2.4.17 is now installed on all systems as the modules RNAfold/2.4.17 and ViennaRNA/2.4.17.  These are different names for the same module.
 

MEGAN version 6.20.17 installed on all systems as module MEGAN/6.20.17.

cutadapt (finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads) version 3.1 installed on all systems as module cutadapt/3.1.

HISAT2 (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) version 2.2.1 installed on all systems as module HISAT2/2.2.1.
 

Unicycler (assembly pipeline for bacterial genomes) version 0.4.8 is now installed as module Unicycler/0.4.8 on all clusters.  This is an alias module for the EasyBuild module Unicycler/0.4.8-gompi-2020a-Python-3.8.2.

SHAPEIT (haplotype estimation for biobank scale datasets) v3.r884.2 (aka SHAPEIT3) is now installed as module SHAPEIT/v3.r884.2.

NCO (The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5) version 4.9.3 installed on all systems as module NCO/4.9.3.
 

quast (Quality Assessment Tool for Genome Assemblies) version 5.0.2 installed on all systems as module quast/5.0.2.

ncview (A netCDF visual browser) version 2.1.7 installed on all systems as module ncview/2.1.7.

MaSuRCA (genome assembly and analysis toolkit) version 3.4.2 installed on all systems as module MaSuRCA/3.4.2.
 

MUMmer (versatile alignment tool for DNA and protein sequences) version 4.0.0rc1 installed on all systems as module MUMmer/4.0.0rc1.
 

schmutzi (Bayesian maximum a posteriori contamination estimate for ancient samples) version 20200706-597c6bc installed on all systems as module schmutzi/20200706-597c6bc.  The previously installed older version schmutzi/20160424 is also enabled.

gcta (analyses to better understand the genetic architecture of complex traits) version 1.93.2beta installed on all systems as module gcta/1.93.2beta.
 

Trinity (assembles transcript sequences from Illumina RNA-Seq data) version 2.11.0 installed on all systems as module trinity/2.11.0.
 

TargetP (predicts the presence of N-terminal presequences: signal peptide (SP), mitochondrial transit peptide (mTP), chloroplast transit peptide (cTP) or thylakoid luminal transit peptide (luTP)) version 2.0 installed on all systems as module TargetP/2.0.

TransDecoder (identifies candidate coding regions within transcript sequences) version 5.5.0 installed on all systems as module TransDecoder/5.5.0.
 

MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) version 0.5.9.4 installed on all systems as module MAGeCK/0.5.9.4.
 

selscan (Positive selection scans on haplotypes.) version 1.3.0 installed on all systems as module selscan/1.3.0.

SweeD (Likelihood-based Selective Sweep Detection) version 4.0.0 installed on all systems as module SweeD/4.0.0.

10X Chromium Cellranger ARC (Cell Ranger single-cell multiome ATAC + Gene Exp.) version 1.0.0 installed on all systems as module cellranger-ARC/1.0.0.  Also installed are Cellranger ARC reference data in cellranger-ARC-data/2020-A.

10X Chromium Cellranger DNA (Cell Ranger DNA single-cell analysis system) version 1.1.0 installed on all systems as module cellranger-DNA/1.1.0.  Also installed are reference data as cellranger-DNA-data/1.0.0.

10X Chromium Cellranger (Cell line analysis system) version 4.0.0 installed on all systems as module cellranger/4.0.0.  Also installed is Cellranger reference data as cellranger-data/4.0.0.
 

Chromium spaceranger (set of analysis pipelines that process Visium spatial RNA-seq output and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices, perform clustering and gene expression analysis, and place spots in spatial context on the slide image) version 1.2.0 installed on all systems as module spaceranger/1.2.0.

Also installed, and loaded by this module as a prerequisite, is Spatial Expression Reference data as module spaceranger-data/2020-A.

NanoPlot (Plotting tool for long read sequencing data and alignments.) version 1.33.1 installed on all systems as module NanoPlot/1.33.1.
 

megahit (MEGAHIT is an ultra-fast and memory-efficient NGS assembler. It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single-cell assembly.) version 1.2.9 installed on all systems as module megahit/1.2.9

mafTools (collection of tools that operate on Multiple Alignment Format (maf) files) version 20170914-82077ac installed on all systems as module mafTools/20170914-82077ac.
 

diamond (sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data) version 2.0.4 installed on all systems as module diamond/2.0.4.
 

QGIS (Create, edit, visualise, analyse and publish geospatial information) version 3.4.12 installed on all systems as module QGIS/3.4.12.
 

Beagle (Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.) version 5.1 installed on all systems as module Beagle/5.1.
https://faculty.washington.edu/browning/beagle/beagle.html

FastQC (A quality control tool for high throughput sequence data) version 0.11.9 installed on all systems as module FastQC/0.11.9.

spades (SPAdes --  St. Petersburg genome assembler -- is an assembly toolkit containing various assembly pipelines.) version 3.14.1 installed on all systems as module spades/3.14.1.

cactus (whole genome alignment) version 1.2.3 installed on all systems as module cactus/1.2.3.  Both the prebuilt Singularity image and locally-built binaries are available.

This is a complicated tool to run.  Please contact support@uppmax.uu.se for additional help.

SAIGE (R package with Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016). It accounts for sample relatedness and is feasible for genetic association tests in large cohorts and biobanks (N > 400,000).) version 0.42.1 installed on all systems as module SAIGE/0.42.1.

The R package SAIGE was removed from R_packages/4.0.0 and moved to this separate module.

jellyfish (tool for fast, memory-efficient counting of k-mers in DNA) version 2.3.0 installed on all systems as module jellyfish/2.3.0.

jellyfish (tool for fast, memory-efficient counting of k-mers in DNA) version 1.1.12 installed on all systems as module jellyfish/1.1.12.

PRISMS-PF (PRedictive Integrated Structural Materials Science–Phase Field) version 2.1.1 is installed on Rackham and Snowy as module PRISMS-PF/2.1.1.
It is a powerful, massively parallel finite element code for conducting phase field and other related simulations of microstructural evolution.

NCL (The NCAR Command Language) version 6.6.2 is installed on Rackham as module NCL-graphics/6.6.2.
It is a free interpreted language designed specifically for scientific data processing and visualization. It can read and write netCDF-3, netCDF-4 classic, netCDF-4, HDF4, binary, and ASCII data. It can read HDF-EOS2, HDF-EOS5, GRIB1, GRIB2, and OGR files (shapefiles, MapInfo, GMT, Tiger).

StringTie (fast and highly efficient assembler of RNA-Seq alignments into potential transcripts) version 2.1.4 installed on all systems as module StringTie/2.1.4.
 

segemehl (segemehl is a software to map short sequencer reads to reference genomes) version 0.3.4 installed on all systems as module segemehl/0.3.4.

WRF (The Weather Research and Forecasting Model) and its pre-processing system (WPS) are installed on Rackham and Snowy as module WRF/4.1.3 and WPS/4.1.3. For usage, run 'module show WRF' or '...WPS'.

vcflib (C++ library for parsing and manipulating VCF files) version 1.0.1 installed on all systems as module vcflib/1.0.1.
 

plink2 (association analysis toolset) version 2.00-alpha-2.3-20200124 installed on all systems as module plink2/2.00-alpha-2.3-20200124.
 

picard (a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF) version 2.23.4 installed on all systems as module picard/2.23.4.

AdmixTools (implements five methods described in Patterson et al. (2012) Ancient admixture in human history) version 7.0.1 installed on all systems as module AdmixTools/7.0.1.
 

MSMC (implements MSMC, a method to infer population size and gene flow from multiple genome sequences) version 1.1.0 installed on all systems as module msmc/1.1.0.

SPRKKR - a spin polarized relativistic Korringa-Kohn-Rostoker (SPR-KKR) code for calculating solid state properties - versions 7.7.1 and 7.7.3 are installed on Rackham and Snowy as modules SPRKKR/7.7.1 and SPRKKR/7.7.3.

ms (generating samples under a Wright-Fisher neutral model) version 20071014 installed on all systems as module ms/20071014.
 

METAL (facilitate meta-analysis of large datasets, such as several whole genome scans) version 2011-03-25 installed on all systems as module METAL/2011-03-25.
 

GenomeTools (free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt) version 1.6.1 installed on all systems as module GenomeTools/1.6.1.
 

RECON (package for automated de novo identification of repeat families from genomic sequences) version 1.08 installed on all systems as module RECON/1.08.  This version uses an updated version of the source.

RepeatScout (tool to discover repetitive substrings in DNA) version 1.0.6 installed on all systems as module RepeatScout/1.0.6.  This version is specially modified to handle multiple sequences.

RepeatScout (tool to discover repetitive substrings in DNA) version 1.0.5 installed on all systems as module RepeatScout/1.0.5.
 

nseg (identifies and masks regions of low complexity in nucleic acid sequences) version 1.0.1 installed on all systems as module nseg/1.0.1.  This is compiled from an updated version of the source originally available from here.
 

TRF (Tandem Repeat Finder, a program to locate and display tandem repeats in DNA sequences) version 4.09.1 installed on all systems as module trf/4.09.1.

tmux (terminal multiplexer) version 3.1b installed on all systems as module tmux/3.1b.

Also provided are older versions tmux/1.9a and tmux/2.5.
 

ont_fast5_api (simple interface to HDF5 files of the Oxford Nanopore .fast5 file format) version 3.1.6 installed on all systems as module ont_fast5_api/3.1.6.
 

MethPipe (computational pipeline for analyzing bisulfite sequencing data (WGBS and RRBS)) version 4.1.1 installed on all systems as module MethPipe/4.1.1.  RADmeth is now included in MethPipe.

NONMEM (very general (non-interactive) model analysis program that can be used to fit models to many different types of data) version 7.4.4 installed on all systems as module nonmem/7.4.4, which compiles with gfortran from gcc/8.3.0, and module nonmem/7.4.4-intel, which compiles with ifort from intel/19.5.  The '-intel' module cannot be used on Bianca.

PsN (Perl-speaks-NONMEM is a collection of Perl modules and programs aiding in the development of non-linear mixed effect models using NONMEM) version 5.0.0 installed on all systems as module PsN/5.0.0.  This is configured to use either nonmem/7.4.3 (PsN name is 7_4_3), nonmem/7.4.3-intel (PsN name is 7_4_3_intel), nonmem/7.4.4 (PsN name is 7_4_4) or nonmem/7.4.4-intel (PsN name is 7_4_4_intel).  7_4_4 is the default.  7_4_3_intel and 7.4.4_intel, like nonmem/7.4.3-intel and nonmem/7.4.4-intel, will not work on bianca.

Pandoc (a Haskell library for converting from one markup format to another, and a command-line tool that uses this library.) version 2.10.1 installed on all systems as module pandoc/2.10.1.
 

Git (Source control management) version 2.28.0 installed on all systems as module git/2.28.0.

Git (Source control management) version 2.24.0 installed on all systems as module git/2.24.0.
 

Tombo (suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data) version 1.5.1 installed on all systems as module Tombo/1.5.1.
 

freebayes (haplotype-based variant detector) version 1.3.2 installed on all systems as module freebayes/1.3.2.
 

Redundans version 0.14a including commits through ffae69e dated 2019 May 09 is now installed on all systems as module Redundans/0.14a-20190509-ffae69e.

LAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. this is the 2.10.1+ update of the local BlastDB tool " 1>&2
BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. this is the 2.10.1+ update of the local BlastDB tool

EnsEMBL-API (The Ensembl Core API (Application Programming Interface) serves as a middle layer between the underlying MySQL database and the user's script. It aims to encapsulate the database layer by providing high level access to the database.) version 94 installed on all systems as module EnsEMBL-API/94.
http://www.ensembl.org/info/docs/api/core/

LDpred (Python based software package that adjusts GWAS summary statistics for the effects of linkage disequilibrium) version 1.0.10 installed on all systems as module LDpred/1.0.10.
 

CITE-seq-Count (python package that allows to count antibody TAGS from a CITE-seq and/or cell hashing experiment) version 1.4.3 installed on all systems as module CITE-seq-Count/1.4.3.
 

HTSeq (Analysing high-throughput sequencing data with Python) version 0.12.4 installed on all systems as module htseq/0.12.4.
 

CMake (open-source, cross-platform family of tools designed to build, test and package software) version 3.17.3 installed on all systems as module cmake/3.17.3.
 

vawk (awk-like VCF parser) version 0.0.1 installed on all systems as module vawk/0.0.1.
 

RepeatMasker (screens DNA sequences for interspersed repeats and low complexity DNA sequences) version 4.1.0 installed on all systems as module RepeatMasker/4.1.0.
 

bwa-meth (fast and accurate alignment of BS-Seq reads) version 0.2.2 installed on all systems as module bwa-meth/0.2.2.
 

MethylDackel (A (mostly) universal methylation extractor for BS-seq experiments) version 0.5.1 installed on all systems as module MethylDackel/0.5.1.
 

BEDTools (the swiss army knife for genome arithmetic) version 2.29.2 installed on all systems as module BEDTools/2.29.2.
 

BRAKER (pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes) version 2.1.5 installed on all systems as module braker/2.1.5.

Note that a copy of the GeneMark licence in the user home directory and a local, writable copy of the augustus config directory are both required to run braker. Help for both is available by following 'module help braker/2.1.5'.

MaxBin (software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm) version 2.2.7 installed on all systems as module MaxBin/2.2.7.
 

CONCOCT (Clustering cONtigs with COverage and ComposiTion) version 1.1.0 installed on all systems as module CONCOCT/1.1.0.
 

CheckM (assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes) version 1.1.2 installed on all systems as module CheckM/1.1.2.
 

MultiQC (aggregate results from bioinformatics analyses across many samples into a single report) version 1.9 installed on all systems as module MultiQC/1.9.
 

MakeHub (Fully automated generation of UCSC assembly hubs) version 1.0.5-1ecd6bb installed on all systems as module MakeHub/1.0.5-1ecd6bb.

The UCSC Kent utilities (Kent bioinformatics utilities) version v398 installed on all systems as module ucsc-utilities/v398.
 

GenomeThreader (software tool to compute gene structure predictions) version 1.7.1 installed on all systems as module GenomeThreader/1.7.1.
 

cdbfasta (Constant DataBase tools for indexing and retrieving records from multi-FASTA or similarly structured files) version 1.00 installed on all systems as module cdbfasta/1.00.
 

ProtHint (pipeline for predicting and scoring hints [in the form of introns, start and stop codons] in the genome of interest by mapping and spliced aligning predicted genes to a database of reference protein sequences) version 2.4.0 installed on all systems as module ProtHint/2.4.0.
 

spaln (stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job) version 2.4.0 installed on all systems as module spaln/2.4.0.
 

HOMER ((Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis) version 4.11 installed on all systems as module HOMER/4.11.  All available data sources are also installed.

RStudio (Integrated development environment for the R language) version 1.2.5042 installed on all systems as module RStudio/1.2.5042.
 

GDAL (translator library for raster and vector geospatial data formats) version 3.1.0 installed on all systems as module GDAL/3.1.0.
 

ROOT (modular scientific software toolkit. It provides all the functionalities needed to deal with big data processing, statistical analysis, visualisation and storage) version 6.20.04 installed on all systems as module ROOT/6.20.04.

PROJ (Cartographic Projections and Coordinate Transformations Library) version 6.3.2 installed on all systems as module PROJ/6.3.2.

rsem (accurate quantification of gene and isoform expression from RNA-Seq data) version 1.3.3 installed on all systems as module rsem/1.3.3.

Stacks (Software pipeline for building loci from short-read sequences) version 2.53 installed on all systems as module Stacks/2.53.

Rust (the Rust programming language and Cargo tools) version 1.43.1 installed on all systems as module rust/1.43.1.

Armadillo version 9.700.2 installed on all systems as module Armadillo/9.700.2. Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. https://sourceforge.net/projects/arma/

Singular (a computer algebra system for polynomial computations, with special emphasis on commutative and non-commutative algebra, algebraic geometry, and singularity theory.) version 4.1.2 installed on all systems as module Singular/4.1.2. https://www.singular.uni-kl.de

GROMACS 2020 installed on Snowy as module gromacs/2020-GPU. GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a GPU enabled build, containing both MPI and threadMPI binaries. http://www.gromacs.org

PhyloBayes MPI (PhyloBayes with MPI support) version 1.8b installed on all systems as module phylobayesmpi/1.8b.  This module loads gcc/9.2.0 and openmpi/3.1.4 and should work equally well on all clusters.
 

ANSYS (engineering simulation software) 2020R1 suite is installed on Rackham as module Ansys/2020R1. ANSYS Fluent, CFX, CEI, ANSYS workbench, and more, are installed. https://www.ansys.com/products/release-highlights

BioPython (Python packages for doing bioinformatics tasks) version 1.76-py3 installed on all systems as module biopython/1.76-py3.  This module loads python/3.7.2 as a prerequisite.

fpc (Free Pascal Compiler) version 3.0.4 installed on all systems as module fpc/3.0.4.

OpenFOAM (a free, open source computational fluid  software package) version v1912 installed on all systems as module OpenFOAM/v1912. https://www.openfoam.com/

OpenFOAM (a free, open source computational fluid  software package) versions 6 and 7 installed on all systems as modules OpenFOAM/6 and OpenFOAM/7. https://www.openfoam.org

Genepop (population genetics software package) version 4.7 installed on all systems as module Genepop/4.7.

XCrySDen (a crystalline and molecular structure visualisation program) versions 1.5.60 and 1.6.2 installed on Rackham as modules XCrySDen/1.5.60 and XCrySDen/1.6.2. http://www.xcrysden.org

Siesta (SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.) version 4.1-MaX-1.0 installed on all systems as module Siesta/4.1-MaX-1.0. https://gitlab.com/siesta-project/siesta/-/tree/MaX-1.0

Siesta (SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.) version 4.1-b4 installed on all systems as module Siesta/4.1-b4. https://gitlab.com/siesta-project/siesta/-/tree/v4.1-b4

diamond (sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data) version 0.9.31 installed on all systems as module diamond/0.9.31. https://github.com/bbuchfink/diamond

Canu (a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION)) version 2.0 installed on all systems as module canu/2.0.  Note that assemblies begun with previous version of Canu (canu/1.x) cannot be continued by canu/2.0.

SpeedSeq (flexible framework for rapid genome analysis and interpretation) version 0.1.2 as of commit 4e60002 on 2018-02-08, is now installed as module SpeedSeq/0.1.2-20180208-4e60002 on all systems.

RAxML (A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies) version 8.2.12-gcc installed on all systems as module raxml/8.2.12-gcc, and with MPI support as raxml/8.2.12-gcc-mpi.

DATES (DATES (Distribution of Ancestry Tracts of Evolutionary Signals) is a method to estimate the time of admixture in ancient DNA samples described in Narasimhan, Patterson et al. 2018) version 753 installed on all systems as module DATES/753.

GSL (Gnu Scientific Library, a numerical library for C and C++ programmers) version 2.5 installed on all systems as module gsl/2.5.

OpenBLAS ( an optimized Basic Linear Algebra Subprograms [BLAS] library based on GotoBLAS2 1.13 BSD version) version 0.2.20 is build in multithreaded and singlethreaded versions and is installed as modules openblas/0.2.20 and openblas/0.2.20-singlethread, respectively, on all systems.

FFTW (C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data) version 3.3.8 installed on all systems as module fftw/3.3.8.

IQ-Tree (efficient software for phylogenomic inference) version 2.0-rc2-omp-mpi installed on all systems as module iqtree/2.0-rc2-omp-mpi.

Barrnap (detect rRNA genes in diverse genomes) version 0.9 installed on all systems as module barrnap/0.9.
 

LUMPY (a general probabilistic framework for structural variant discovery) version 0.3.0 installed on all systems as module LUMPY/0.3.0.

sambamba (SAM file processing) version 0.7.1 installed on all systems as module sambamba/0.7.1.

fastp (fast all-in-one preprocessing for FastQ files) version 0.20.0 installed on all systems as module fastp/0.20.0.
 

LINKS (Long Interval Nucleotide K-mer Scaffolder) version 1.8.7 installed on all systems as module LINKS/1.8.7.

ARCS (scaffold genome sequence assemblies using linked read sequencing data) version 1.1.1 installed on all systems as module ARCS/1.1.1.  This module also loads LINKS/1.8.7 and tigmint/1.1.2.

swig (code generator for connecting C/C++ with other programming languages) version 3.0.12 installed on all systems as module swig/3.0.12.

GAA (merge assemblies) version 1.1 installed on all systems as module GAA/1.1.

NCO (toolkit manipulates and analyzes data stored in netCDF-accessible formats) versions 4.8.1 and 4.9.2 are now available as modules NCO/4.8.1 and NCO/4.9.2 on all systems.

ABINIT (software suite to calculate the optical, mechanical, vibrational, and other observable properties of materials) version 8.10.3 is now installed as module ABINIT/8.10.3 on all systems.

NLopt (a library for nonlinear local and global optimization, for functions with and without gradient information. It is designed as a simple, unified interface and packaging of several free/open-source nonlinear optimization libraries.) version 2.6.1 installed on all systems as module NLopt/2.6.1.

deepTools (tools to process and analyze deep sequencing data) version 3.3.2 installed on all systems as module deepTools/3.3.2.

MACS (Model-based Analysis of ChIP-Seq) version 2.2.6 is now installed as module MACS/2.2.6 on all systems.

PCAngsd (framework for analyzing low depth NGS data in heterogeneous populations using PCA) version 0.982 installed on all systems as module PCAngsd/0.982.

SLiM (evolutionary genetic forward simulations) version 3.3.2 is now installed as module SLiM/3.3.2 on all systems.

SLiM (evolutionary genetic forward simulations) 2.6 has been installed as module SLiM/2.6 on all systems.

Beagle (general purpose library for evaluating the likelihood of sequence evolution on trees) version 3.1.2 installed on all systems as module beagle/3.1.2.

Beast2 (Bayesian Evolutionary Analysis by Sampling Trees) version 2.6.2pre installed on all systems as module beast2/2.6.2pre.

PRSice (A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores) version 2.2.11.b installed on all systems as module PRSice/2.2.11.b.

CD-Hit (clustering and deduplication of a wide variety of sequence data) version 4.8.1 installed on all systems as module cd-hit/4.8.1.

MaSuRCA (assembler for short reads, long reads, and hybrid datasets) version 3.3.5 installed on all systems as module MaSuRCA/3.3.5.

Quickmerge (simple and fast metassembler and assembly gap filler designed for long molecule based assemblies) version 0.3-9233726 installed on all systems as module quickmerge/0.3-9233726.  By default, the module loads MUMmer74.0.0beta2 for alignment, to enable multithreading.  If an earlier, nonmultithreaded MUMmer is desired, load the appropriate MUMmer module after loading this module.

Pacific Biosciences' bam2fastq (converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files) version 1.3.0-80dbf79 (release 1.3.0 updated through git commit 80dbf79) installed on all systems as module bam2fastx/1.3.0-80dbf79.

AUGUSTUS (find genes and their structures in one or more genomes) version 3.3.3 installed on all systems as module augustus/3.3.3.

Salmon version 1.1.0, a tool for transcript quantification from RNA-seq data, has been installed on all systems as module Salmon/1.1.0 . 

Subread (high-performance read alignment, quantification and mutation discovery) version 2.0.0 installed on all systems as module subread/2.0.0.

BamBam (numerous tools for analyzing DNA next-generation sequencing data: calling SNPs and indels, identifying large scale deletions, tabulating counts of mapped reads, methylation analysis, and more) version 1.4 is now available as module bambam/1.4 on all systems.

LDpred (software package that adjusts GWAS summary statistics for the effects of linkage disequilibrium) version 1.0.11 has been installed as module LDpred/1.0.11 on all systems.

Samtools, BCFtools and HTSlib (extremely useful bioinformatics tools) versions 1.10 have been installed as modules samtools/1.10, bcftools/1.10 and htslib/1.10 on all systems.  These have all been compiled with libcurl, AWS S3, GCS and HTSlib plugins enabled.  BCFtools has been compiled with Perl filters enabled and GSL support, which adds the +polysomy plugin.

10X Chromium Space Ranger (set of analysis pipelines that process Visium spatial RNA-seq output and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices, perform clustering and gene expression analysis, and place spots in spatial context on the slide image) version 1.0.0 is now installed as spaceranger/1.0.0 on all systems.  Also installed is the data module spaceranger-data/1.0.0, which provides Visium Dual Index sets.  Reference data for this module is provided by the cellranger-data/3.0.0 module.

PLplot (a cross-platform software package for creating scientific plots whose (UTF-8) plot symbols and text are limited in practice only by what Unicode-aware system fonts are installed on a user's computer) version 5.15.0 is now installed on all clusters as two modules: PLplot/5.15.0, with default wxWidgets support, and PLplot/5.15.0-old_wxWidgets, which was built with the  -DOLD_WXWIDGETS:BOOL=ON option which incorporates an older wxWidgets toolkit driver required by the Gnu Data Language gdl/1.0.0-rc.1 module.

HDF4 (data file format) version 4.2.14 compiled with gcc/6.3.0 is now installed as module hdf4/4.2.14-gcc6.3.0 on all systems.

pslib (C-library to create PostScript files on the fly, offering many drawing primitives including inclusion of PNG and EPS images and very sophisticated text rendering) version 0.4.6 is now installed on all systems as module pslib/0.4.6.

WxWidgets (C++ library that lets developers create applications for Windows, macOS, Linux and other platforms with a single code base) version 3.1.3 is now installed on all systems in three different modules, each supporting a different toolkit.  wxWidgets/3.1.3-gtk2 supports the GTK2 toolkit, wxWidgets/3.1.3-gtk3 supports the GTK3 toolkit, and wxWidgets/3.1.3-qt5 supports the Qt5 toolkit.

Patchelf (small executable patcher) version 0.10 is now installed on all systems as module patchelf/0.10.

Gnu Data Language version 1.0.0-rc.1 is now installed on all systems as module gd0/1.0.0-rc.1.

git-lfs (Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com or GitHub Enterprise.) version 2.9.1 installed on all systems as module git-lfs/2.9.1.

Git (Source control management) version 2.24.0 installed on all systems as module git/2.24.0.

SHAPELIB (library provides the ability to write simple C programs for reading, writing and updating (to a limited extent) ESRI Shapefiles, and the associated attribute file (.dbf)) version 1.5.0 is now installed on all systems as module SHAPELIB/1.5.0.

Qhull (computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram) version 2019.1 installed on all systems as module Qhull/2019.1.

SignalP (predicts the presence of signal peptides and the location of their cleavage sites in proteins from Archaea, Gram-positive Bacteria, Gram-negative Bacteria and Eukarya) version 5.0b installed on all systems as module SignalP/5.0b.

10X Genomics' Chromium Cell Ranger ATAC (set of analysis pipelines that process Chromium Single Cell ATAC data) version 1.2.0 is now installed on all systems as module cellranger-ATAC/1.2.0.

Cell Ranger ATAC reference data is also available in the data module cellranger-ATAC-data/1.2.0.  This module is loaded with the cellranger-ATAC/1.2.0 module.

Diamond (sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data) version 0.9.29 installed on all systems as module diamond/0.9.29.