bubblewrap (Unprivileged sandboxing) version 0.6.2 installed on all systems as module bubblewrap/0.6.2. Note that this is not installed setuid, which may be insufficient for some tools.
 

ORFfinder (ORF finder searches for open reading frames (ORFs) in a DNA sequence) version 0.4.3 installed on all systems as module ORFfinder/0.4.3.
 

fastsimcoal (fast sequential markov coalescent simulation of genomic data under complex evolutionary models) version 2.7.9 installed on all systems as module fastsimcoal/2.7.9.
 

Arlequin (An Integrated Software for Population Genetics Data Analysis) version 3.5.2.2 installed on all systems as module Arlequin/3.5.2.2. This module includes the latest arlsumstat executable.
 

ABCtoolbox (Performs Approximate Bayesian Computation (ABC) estimations using various recently published algorithms including MCMC without likelihood and Population Monte Carlo) version 20131120 installed on all systems as module ABCtoolbox/20131120.
 

julia (high-level, high-performance dynamic language for technical computing.) versionstems as module julia/1.7.2.

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 2.4.9 installed on all systems as module spaln/2.4.9.
 

slurm-drmaa (DRMAA for Slurm Workload Manager (Slurm) is an implementation of Open Grid Forum Distributed Resource Management Application API (DRMAA) version 1 for submission and control of jobs to Slurm. Using DRMAA, grid applications builders, portal developers and ISVs can use the same high-level API to link their software with different cluster/resource management systems. Built against SLURM 21.08.8) version 1.1.3-slurm21.08.8 installed on all systems as module slurm-drmaa/1.1.3-slurm21.08.8.
 

KrakenUniq (confident and fast metagenomics classification using unique k-mer counts) version 0.6 installed on all systems as module KrakenUniq/0.6.
 

bwa-mem2 (the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.) version 2.2.1-20211213-edc703f installed on all systems as module bwa-mem2/2.2.1-20211213-edc703f.

cutadapt (finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads) version 4.0 installed on all systems as module cutadapt/4.0.
 

SQuIRE (Software for Quantifying Interspersed Repeat Expression) version 885bf4d-20190301 installed on all systems as module SQuIRE/885bf4d-20190301.
 

BioBloomTools (Create Bloom filters for a given reference and then use it to categorize sequences) version 2.3.3-20210218-151b0c0 installed on all systems as module BioBloomTools/2.3.3-20210218-151b0c0.
 

LLVM (The LLVM package contains a collection of modular and reusable compiler and toolchain technologies.) version 13.0.1 installed on all systems as module LLVM/13.0.1.

pblat-cluster (blat with cluster parallel hybrid computing support) version 1.1 installed on all systems as module pblat-cluster/1.1.
 

pblat (parallelized blat with multi-threads support) version 2.5 installed on all systems as module pblat/2.5.
 

binutils (a collection of binary tools, built with plugin support) version 2.38 installed on all systems but miarka as module binutils/2.38.
 

BlobToolKit (A new implementation of BlobTools with support for interactive data exploration via the BlobToolKit viewer) version 3.1.0 installed on all systems as module BlobToolKit/3.1.0.

gdb version 11.2 installed on all systems as module gdb/11.2.

Kraken (taxonomic sequence classification system) version 1.1.1-20210927-375654f installed on all systems as module Kraken/1.1.1-20210927-375654f.

Note that Kraken is superseded by Kraken2, and the latest Kraken2 module, for example Kraken2/2.1.2-20211210-4f648f5, should be used in preference to this.

The libicu library on EL8 has been updated to v60 with no legacy libraries for v50. The libicu/5.2-4 module contains the contents of libicu.x86_64 and libicu-devel.x86_64 from CentOS7 for use by executables running on an EL8 system. Executables using these libraries should have their RPATH information updated to point to subdirectories within this module, and the module itself can also be used as a development dependency.

The readline library on EL8 has been updated to v7 with no legacy libraries for v6. The readline/6.2-11 module contains the contents of readline.x86_64 and readline-devel.x86_64 from CentOS7 for use by executables running on an EL8 system. Executables using these libraries should have their RPATH information updated to point to subdirectories within this module, and the module itself can also be used as a development dependency.

python_ML_packages (Python package installation) version 3.9.5-gpu installed on all systems as module python_ML_packages/3.9.5-gpu.

ATLAS_aDNA (ATLAS stands for Analysis Tools for Low-coverage and Ancient Samples. These tools cover all programs necessary to obtain variant calls, estimates of heterozygosity and more from a BAM file.) version 0.9.9 installed on all systems as module ATLAS_aDNA/0.9.9.

fastq_demux (A simple program to demultiplex Illumina FASTQ files based on barcodes in the FASTQ headers) version 20200918-1e2c079 installed on all systems as module fastq_demux/20200918-1e2c079.

PsN (Perl-speaks-NONMEM \(PsN\) is a collection of Perl modules and programs aiding in the development of non-linear mixed effect models using NONMEM) version 5.3.0 installed on all systems as module PsN/5.3.0.

metaMATE version 20220327-3cdacd7 installed on all systems as module metaMATE/20220327-3cdacd7.

SDSL (a powerful and flexible C++11 library implementing succinct data structures) version 2.1.1 installed on all systems as module SDSL/2.1.1.
 

Sparsehash version 2.0.4 installed on all systems as module sparsehash/2.0.4.
 

MUSCLE (Multiple sequence alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures) version 5.1 installed on all systems as module muscle/5.1.
 

tRNAscan-SE (Improved Detection and Functional Classification of Transfer RNA Genes) version 2.0.9 installed on all systems as module tRNAscan-SE/2.0.9.
 

infernal ("INFERence of RNA ALignment" -- is for searching DNA sequence databases for RNA structure and sequence similarities) version 1.1.4 installed on all systems as module infernal/1.1.4.
 

VESPA (The VESPA (Very large-scale Evolution and Selective Pressure analyses) toolkit is a collection of commands designed to simplify molecular evolutionary analyses.) version 1.0.1 installed on all systems as module VESPA/1.0.1.

https://vespa-evol.readthedocs.io/en/latest/

CPLEX Optimization Studio version 20.10 is installed on all systems as module CPLEXOptimizationStudio/20.10. CPLEX Optimizer provides flexible, high-performance mathematical programming solvers for linear programming, mixed integer programming, quadratic programming and quadratically constrained programming problems. These solvers include a distributed parallel algorithm for mixed integer programming to leverage multiple computers to solve difficult problems.

CPLEX Optimization Studio version 12.9.0 installed on all systems as module CPLEXOptimizationStudio/12.9.0. CPLEX Optimizer provides flexible, high-performance mathematical programming solvers for linear programming, mixed integer programming, quadratic programming and quadratically constrained programming problems. These solvers include a distributed parallel algorithm for mixed integer programming to leverage multiple computers to solve difficult problems.
 

CAMMiQ (CAMMiQ is a software tool for microbial identification and quantification.) version 20211015-6142150 installed on all systems as module CAMMiQ/20211015-6142150.
 

fastp version 0.23.2 installed on all systems as module fastp/0.23.2.  fastp is a tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.

The data module Pfam/35.0, containing protein families that are part of the 35.0 release of Pfam, is now available. The earlier releases Pfam/2011, Pfam/28.0 and Pfam/31.0 are also now available as data modules.

RStudio (Integrated development environment for the R language) version 2022.02.0-443 installed on all systems as module RStudio/2022.02.0-443.
 

BclConverter (converts per cycle binary data output by Illumina sequencers containing basecall files and quality scores to per read FASTQ files) version 3.9.3 installed on all systems as module BclConverter/3.9.3.
 

SuperLU (a set of subroutines to solve a sparse linear system A*X=B) version 5.2.1 is now installed with both shared and static libraries as module SuperLU/5.2.1.

PsN (Perl-speaks-NONMEM \(PsN\) is a collection of Perl modules and programs aiding in the development of non-linear mixed effect models using NONMEM) version 5.3.0 installed on all systems as module PsN/5.3.0.

fastq_demux (A simple program to demultiplex Illumina FASTQ files based on barcodes in the FASTQ headers) version 20200918-1e2c079 installed on all systems as module fastq_demux/20200918-1e2c079.

atlas (ATLAS stands for Analysis Tools for Low-coverage and Ancient Samples. These tools cover all programs necessary to obtain variant calls, estimates of heterozygosity and more from a BAM file.) version 0.9.9 installed on all systems as module atlas/0.9.9.

GAAS (Suite of tools related to Genome Assembly Annotation Service tasks) version 1.2.0 installed on all systems as module GAAS/1.2.0.
 

metaSNV (a metagenomic SNV calling pipeline.) version 2.0.1 installed on all systems as module metaSNV/2.0.1.

metaSNV (a metagenomic SNV calling pipeline.) version 1.0.3 installed on all systems as module metaSNV/1.0.3.

pandoc (Pandoc is a Haskell library for converting from one markup format to another, and a command-line tool that uses this library.) version 2.17.1.1 installed on all systems as module pandoc/2.17.1.1.
 

RevBayes (Bayesian phylogenetic inference using probabilistic graphical models and an interactive language.) version 1.1.1-mpi installed on all systems as module RevBayes/1.1.1-mpi.

RevBayes (Bayesian phylogenetic inference using probabilistic graphical models and an interactive language.) version 1.1.1 installed on all systems as module RevBayes/1.1.1.

boost (free peer-reviewed portable C++ source libraries) version 1.78.0_gcc11.2.0 installed on all systems as module boost/1.78.0_gcc11.2.0.

boost (free peer-reviewed portable C++ source libraries) version 1.78.0-gcc11.2.0_mpi4.1.2 installed on all systems as module boost/1.78.0-gcc11.2.0-mpi4.1.2.

The package Intel OneAPI with subpackages are installed on all systems

CMake (open-source, cross-platform family of tools designed to build, test and package software) version 3.22.2 installed on all systems as module cmake/3.22.2.
 

[apps] gromacs/2021.5.th installed on Rackham and Snowy

Kraken2 (a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds) version 2.1.2-20211210-4f648f5 installed on all systems as module Kraken2/2.1.2-20211210-4f648f5. This version is identical to version 2.1.2, but with a couple of small changes to account for changes in the methods of accessing some remote databases.
 

DIAMOND (sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data) version 2.0.14 installed on all systems as module diamond/2.0.14.
 

The NCBI taxonomy databases are now available through the newly installed data module ncbi_taxonomy/latestX. This module defines the environment variable NCBI_TAXONOMY_ROOT, which contains the location of the local UPPMAX mirror of the NCBI taxonomy databases located at /sw/data/ncbi_taxonomy/latest. See https://www.ncbi.nlm.nih.gov/guide/taxonomy/ for more on the internal contents of the databases.

[apps] Amber, a suite of biomolecular simulation programs, version 20 is installed on Rackham and Snowy (GPU) as module Amber/20 for Rackham and Amber/20-GPU for Snowy GPU with CUDA support. 

FusionCatcher (Finder of somatic fusion-genes in RNA-seq data) version 1.33 installed on all systems as module FusionCatcher/1.33.
 

ORCA version 5.0.2 is installed on Rackham and Snowy as module ORCA/5.0.2. ORCA is a quantum-chemical software package consisting of methods in the fields of density functional theory as well as correlated wave-function based methods.

MultiQC (Aggregate results from bioinformatics analyses across many samples into a single report) version 1.12 installed on all systems as module MultiQC/1.12.
 

ngsLD (Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework) version 1.1.1 installed on all systems as module ngsLD/1.1.1.
 

slurm-drmaa (DRMAA for Slurm Workload Manager (Slurm) is an implementation of Open Grid Forum Distributed Resource Management Application API (DRMAA) version 1 for submission and control of jobs to Slurm. Using DRMAA, grid applications builders, portal developers and ISVs can use the same high-level API to link their software with different cluster/resource management systems. Built against SLURM 19.05.8) version 1.1.3-slurm19.05.8 installed on all systems as module slurm-drmaa/1.1.3-slurm19.05.8. Version slurm-drmaa/1.1.3-slurm21.08.2 is installed on miarka.

PEPPER-Margin-DeepVariant (PEPPER is a genome inference module based on recurrent neural networks that enables long-read variant calling and nanopore assembly polishing in the PEPPER-Margin-DeepVariant pipeline.) version r0.4 installed on all systems as module PEPPER-Margin-DeepVariant/r0.4.

Nextflow (A DSL for data-driven computational pipelines http://nextflow.io) version 21.10.6 installed on all systems as module Nextflow/21.10.6.

UMAnN (\(the HMP Unified Metabolic Analysis Network\) is a method for efficiently and accurately profiling the abundance of microbial metabolic pathways and other molecular functions from metagenomic or metatranscriptomic sequencing data.) version 3.0.0.a.4 installed on all systems as module HUMAnN/3.0.0.a.4.

PEPPER-Margin-DeepVariant (PEPPER is a genome inference module based on recurrent neural networks that enables long-read variant calling and nanopore assembly polishing in the PEPPER-Margin-DeepVariant pipeline.) version r0.7 installed on all systems as module PEPPER-Margin-DeepVariant/r0.7.

DeepVariant (DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file.) version 1.3.0 installed on all systems as module DeepVariant/1.3.0.

PROJ (Cartographic Projections and Coordinate Transformations Library) version 8.1.0 installed on all systems as module PROJ/8.1.0.
 

rMATS-turbo (computational tool to detect differential alternative splicing events from RNA-Seq data.) version 4.1.2 installed on all systems as module rMATS-turbo/4.1.2.
 

SvABA (Structural variation and indel detection by local assembly) version 1.1.3-20201112-0f60e36 installed on all systems as module SvABA/1.1.3-20201112-0f60e36.
 

SNP2HLA (a tool to impute amino acid polymorphisms and single nucleotide polymorphisms in human luekocyte antigenes (HLA) within the major histocompatibility complex (MHC) region in chromosome 6) version 1.0.3 installed on all systems as module SNP2HLA/1.0.3.
 

CNVnator (a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads) version 0.4.1-20200707-c73786d installed on all systems as module CNVnator/0.4.1-20200707-c73786d.
 

NextGenMap (flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime) version 0.5.5 installed on all systems as module NextGenMap/0.5.5. This is configured to be able to take advantage of GPU-containing nodes on snowy and bianca.
 

MultiBUGS (a software package for performing Bayesian inference. It builds on the existing algorithms and tools in OpenBUGS and WinBUGS, and so is applicable to the broad range of statistical models that can be fitted using BUGS-language software, but automatically parallelises the MCMC algorithm to dramatically speed up computation.) version 2.0 installed on all systems as module MultiBUGS/2.0.
 

paml (PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.) version 4.9j installed on all systems as module paml/4.9j.
 

Tesseract (Open-source optical character recognition (OCR) engine) version 4.1.3 installed on all systems as module tesseract/4.1.3.
 

gmap-gsnap (Genomic Mapping and Alignment Program for mRNA and EST Sequences) versions 2017-11-15 2021-12-17 are installed on all systems as modules gmap-gsnap/2017-11-15 and gmap-gsnap/2021-12-17.
 

TSEBRA (a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons, developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies) version 1.0.3-20211126-336c380 installed on all systems as module TSEBRA/1.0.3-20211126-336c380.
 

git (Source control management) version 2.34.1 installed on all systems as module git/2.34.1.
 

RAxML-NG (a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion) version 1.1.0 installed on all systems as module RAxML-NG/1.1.0, statically linked with shared-memory threads support, and RAxML-NG/1.1.0-mpi, with parallelism support provided via OpenMPI.
 

paraview (ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. ) version 5.9.1 installed on all systems as module paraview/5.9.1. Start tool with "vgl_paraview".
 

Julia (a high-level, high-performance dynamic language for technical computing.) version 1.6.3 installed on all systems as module julia/1.6.3.
 

julia (Julia is a high-level, high-performance dynamic language for technical computing.) version 1.0.5_LTS installed on all systems as module julia/1.0.5_LTS.
 

Salmon (a tool for wicked-fast transcript quantification from RNA-seq data) version 1.6.0 installed on all systems as module Salmon/1.6.0.
 

MetaCRAST (MetaCRAST (Metagenomic CRISPR Reference-Aided Search Tool) is a tool to detect CRISPR arrays in raw, unassembled metagenomes.) version 20200310-ed82df4 installed on all systems as module MetaCRAST/20200310-ed82df4.

Guppy (Oxford Nanopore neural-net basecaller, GPU-enabled) version 5.0.16 installed on the Bianca and Snowy systems as module Guppy/5.0.16-gpu.

Guppy (Oxford Nanopore neural-net basecaller, CPU only) version 5.0.16 installed on all systems as module Guppy/5.0.16-cpu.

bismark (Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step.) version 0.23.1 installed on all systems as module bismark/0.23.1

RSPt is a code for electronic structure calculations based on the Full-Potential Linear Muffin-Tin Orbital (FP-LMTO) method. Version dated 2021-10-04 installed on all systems as module RSPt/2021-10-04.

Chromium-cellranger (Cell line analysis system) version 6.1.2 installed on all systems as module cellranger/6.1.2.

fastqtk (fast and lightweight tool for interleaving/deinterleaving/counting/trimming FASTQ files) version 0.27 installed on all systems as module fastqtk/0.27.
 

vim (VIM, the editor) version 8.2.3701 installed on all systems as module vim/8.2.3701.
 

QuantumESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. Versions 6.8 installed on Rackham and Snowy as module QuantumESPRESSO/6.8 and QuantumESPRESSO/6.7MaX-Release, respectively.

trimmomatic (Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.) version 0.39 installed on all systems as module trimmomatic/0.39.

fastp (fast all-in-one preprocessing for FastQ files) version 0.23.1 installed on all systems as module fastp/0.23.1.
 

nasm (Netwide Assembler (NASM), an asssembler for the x86 CPU architecture portable to nearly every modern platform, and with code generation for many platforms old and new) version 2.15.05 installed on all systems as module nasm/2.15.05.
 

Conterminator (Conterminator is an efficient method for detecting incorrectly labeled sequences across kingdoms by an exhaustive all-against-all sequence comparison.) version 20200601-570993b installed on all systems as module Conterminator/20200601-570993b.

R_packages (Omnibus package containing installations of as many R packages from CRAN, BioConductor and other user-requested sources as can be reasonably installed) version 4.1.1 installed on all systems as module R_packages/4.1.1.

Cromwell (Cromwell is an open-source Workflow Management System for bioinformatics) version 71 installed on all systems as module Cromwell/71.

vsearch (Open-source alternative to USEARCH, supporting: supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting; FASTQ file analysis, filtering, conversion and merging of paired-end reads) version 2.18.0 installed on all systems as module vsearch/2.18.0.
 

Bamsurgeon (tools for adding mutations to .bam files, used for testing mutation callers) version 1.3 installed on all systems as module Bamsurgeon/1.3.

pixy (pixy is a command-line tool for painlessly estimating average nucleotide diversity within (π) and between (dxy) populations from a VCF) version 1.2.5.beta1 installed on all systems as module pixy/1.2.5.beta1.

htslib (Tools for working with SAM/BAM/variant files) version 1.14 installed on all systems as module htslib/1.14.

bcftools (Tools for working with variant files) version 1.14 installed on all systems as module bcftools/1.14.

NeuSomatic (NeuSomatic is based on deep convolutional neural networks for accurate somatic mutation detection.) version 0.2.1 installed on all systems as module NeuSomatic/0.2.1.

samtools (Tools for working with SAM/BAM/variant files) version 1.14 installed on all systems as module samtools/1.14

pysam (Pysam is a python module for reading and manipulating files in the SAM/BAM format) version 0.17.0-python3.9.5 installed on all systems as module pysam/0.17.0-python3.9.5.

VIBRANT (Virus Identification By iteRative ANnoTation) version 1.2.1 installed on all systems as module VIBRANT/1.2.1.

WPS-geog (WPS static geodata) version 4 installed on Rackham and Snowy as module WPS-geog/4.

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 2.2 installed on all systems as module canu/2.2

Flye (de novo assembler for single molecule sequencing reads\, such as those produced by PacBio and Oxford Nanopore Technologies) version 2.9 installed on all systems as module Flye/2.9.

SMARTdenovo (SMARTdenovo is a de novo assembler for PacBio and Oxford Nanopore (ONT) data.) version 20210224-8488de9 installed on all systems as module SMARTdenovo/20210224-8488de9.

NextDenovo (NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT)) version 2.5.0 installed on all systems as module NextDenovo/2.5.0.

STAR (Spliced Transcripts Alignment to a Reference) version 2.7.9a installed on all systems as module star/2.7.9a.
 

rclone (a command line program to manage files on cloud storage, supporting over 40 cloud storage products) version 1.56.2 installed on all systems as module rclone/1.56.2.

NextDenovo (NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT)) version 2.4.0 installed on all systems as module NextDenovo/2.4.0

phaser (phasing and Allele Specific Expression from RNA-seq) version 20210423-5d4926d installed on all systems as module phaser/20210423-5d4926d

Racon (Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads) version 1.4.21 installed on all systems as module Racon/1.4.21.
 

UCSC utilities (Kent bioinformatics utilities) version v421 installed on all systems as module ucsc-utilities/v421.
 

snakemake (The Snakemake workflow management system is a tool to create reproducible and scalable data analyses) version 6.9.1 installed on all systems as module snakemake/6.9.1.

NgsRelate (Infers relatedness, inbreeding coefficients and many other summary statistics for pairs of individuals from low coverage Next Generation Sequencing (NGS) data by using genotype likelihoods instead of called genotypes. ) version 2.0 installed on all systems as module NgsRelate/2.0.
 

maker (Portable and easily configurable genome annotation pipeline) version 3.01.04 installed on all systems as module maker/3.01.04

nf-core-pipelines (pipelines that are currently available as part of nf-core) version latest installed on all systems as module nf-core-pipelines/latest

alphafold (This package provides an implementation of the inference pipeline of AlphaFold v2.0.) version 2.0.0 installed on all systems as module alphafold/2.0.0

MACS (Model-based Analysis of ChIP-Seq) version 3.0.0a6 installed on all systems as module MACS/3.0.0a6.

IMAP (Chromosome-level genome assembler combining multiple de novo assemblies) version 1.0 installed on all systems as module IMAP/1.0.
https://github.com/jkimlab/IMAP
rackham, irma, bianca, snowy
1.0.0

trinity (assembles transcript sequences from Illumina RNA-Seq data) version 2.13.2 installed on all systems as module trinity/2.13.2.
 

R (free software environment for statistical computing and graphics) version 4.1.1 installed on all systems as module R/4.1.1. Its version of the omnibus R_packages module is not yet installed.

cairo (a 2D graphics library with support for multiple output devices) version 1.17.4 installed on all systems as module cairo/1.17.4.
 

A full installation of TeX Live (a straightforward way to get up and running with the TeX document production system) version 2021 installed on all systems as module texlive/2021.

SAIGE (an 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 0.44.6.5 installed on all systems as module SAIGE/0.44.6.5.
 

[libs] ARPACK-NG/3.8.0 installed on all systems
ARPACK-NG (ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.) version 3.8.0 installed on all systems as module ARPACK-NG/3.8.0.
https://github.com/opencollab/arpack-ng

SuperLU (a set of subroutines to solve a sparse linear system A*X=B.) version 5.2.1 installed on all systems as module SuperLU/5.2.1.
 

[bio] medaka/1.4.3 Installed on all systems

SymEngine (standalone fast C++ symbolic manipulation library) version 0.7.0 installed on all systems as module SymEngine/0.7.0.

[bio] nf-core/2.1 Installed on all systems

[bio] InterProScan/5.52-86.0 Installed on all systems

Stacks version 2.59 installed on all systems as module Stacks/2.59.

TSEBRA (a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons, developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies) version 1.0.2-20210716-1f167ad installed on all systems as module TSEBRA/1.0.2-20210716-1f167ad.
 

braker (pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes) version 2.1.6 installed on all systems as module braker/2.1.6.
 

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 2.6.0 installed on all systems as module ProtHint/2.6.0.
 

GeneMark (Gene prediction in eurkaryotes) version 4.68-es installed on all systems as module GeneMark/4.68-es.
 

A workflow for ancient DNA placement into reference phylogenies.

Efficient likelihood calculations to place samples into a phylogenetic tree. In particular, phynder was originally designed for placing male ancient DNA samples into the Y chromosome phylogeny, when there are arbitrarily high rates of missing data. It has also been used for assigning ancient samples to whole mitochondrial genome phylogenies.

plumed version 2.7.1-gcc installed on Rackham as module plumed/2.7.1-gcc.
https://www.plumed.org

cp2k (CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems.) version 8.1-gcc installed on all systems as module cp2k/8.1-gcc.
https://www.cp2k.org/

MultiQC (Aggregate results from bioinformatics analyses across many samples into a single report) version 1.11 installed on all systems as module MultiQC/1.11.
 

IMPUTE5 (IMPUTE 5 is a genotype imputation method that can scale to reference panels with millions of samples.) version 1.1.5 installed on all systems as module IMPUTE5/1.1.5.
https://jmarchini.org/software/#impute-5

julia version 1.6.1 installed on all systems as module julia/1.6.1

bonito version 0.3.7-cpu installed on all systems as module bonito/0.3.7-cpu.
https://github.com/nanoporetech/bonito/issues/70

Python (programming language plus a handful of widely used packages) version 3.9.5 installed on all systems as module python/3.9.5. The module python3/3.9.5 is available that will not conflict with a python/2.y.z module. For a list of installed packages, including numpy and scipy, see the module help or run 'pip3 list' when the module is loaded.

[apps] emacs/27.2 installed on all systems

pizzly (Fast fusion detection using kallisto) version 0.37.3 installed on all systems as module pizzly/0.37.3.

EDirect (EDirect provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a Unix terminal window) version 15.1 installed on all systems as module EDirect/15.1.
 

gffread (GFF/GTF utility providing format conversions, filtering, FASTA sequence extraction and more) version 0.12.6 installed on all systems as module gffread/0.12.6.
 

MPC (library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result) version 1.2.1 installed on all systems as module MPC/1.2.1.
 

The previous Kmer Analysis Toolkit module KAT/2.4.2, based on python/3.5.0, is moved to the name KAT/2.4.2_py3.5.0 and deprecated. The previous module KAT/2.4.2_py3.7.2 is renamed KAT/2.4.2, and KAT/2.4.2_py3.7.2 is an alias.

ANNOVAR (an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes) version 2020.06.08 installed on all systems as module annovar/2020.06.08.  The databases have been organised into data modules and the latest are found in the data module annovar_data/2021.05.18.

FALCON (PacBio diploid assembler) version 2018.31.08-03.06 installed on all systems as module FALCON/2018.31.08-03.06.

Trinotate (comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms) version 3.2.2 installed on all systems as module trinotate/3.2.2.
 

OpenBLAS (an optimized BLAS library based on GotoBLAS2 1.13 BSD version) version 0.3.15 is now installed in several module versions on all clusters.

openblas/0.3.15 has standard multithreading support. openblas/0.3.15-openmp supports OpenMP multithreading.  openblas/0.3.15-singlethread does not have multithreading support.

bison (a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables) version 3.7.6 installed on all systems as module bison/3.7.6.
 

flex (The Fast Lexical Analyzer - scanner generator for lexing in C and C++) version 2.6.4 installed on all systems as module flex/2.6.4.
 

CheckM (Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes) version 1.1.3 installed on all systems as module CheckM/1.1.3.
 

metaWRAP (MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis) version 1.3.2 installed on all systems as module metaWRAP/1.3.2.

SMC++ (infers population history from whole-genome sequence data) version 1.15.2 installed on all systems as module SMC++/1.15.2.
 

ArrowGrid (parallel wrapper around the Arrow consensus framework within the SMRT Analysis Software) version 20191022-9759eb1 installed on all systems as module ArrowGrid/20191022-9759eb1. This module has rough support for submitting multiple jobs through SLURM and we have attempted to give appropriate defaults to its SLURM parameters. See its documentation for specifying a CONFIG file.

pbbam (software package provides components to create, query, & edit PacBio BAM files and associated indices, including a core C++ library, bindings for additional languages, and command-line utilities) version 1.6.0 installed on all systems as module pbbam/1.6.0.
 

ninja (a small build system with a focus on speed) version 1.10.0 installed on all systems as module ninja/1.10.0.
 

meson (open source build system meant to be both extremely fast, and, even more importantly, as user friendly as possible) version 0.57.2 installed on all systems as module meson/0.57.2.
 

snippy (finds SNPs between a haploid reference genome and your NGS sequence reads.) version 4.6.0 installed on all systems as module snippy/4.6.0.
 

HUMAnN ((the HMP Unified Metabolic Analysis Network) is a method for efficiently and accurately profiling the abundance of microbial metabolic pathways and other molecular functions from metagenomic or metatranscriptomic sequencing data.) version 3.0 installed on all systems as module HUMAnN/3.0.
 

KneadData (is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.) version 0.10.0 installed on all systems as module KneadData/0.10.0.
 

PhyloPhlAn (is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes.) version 3.0.2 installed on all systems as module PhyloPhlAn/3.0.2.
 

MetaPhlAn3 (is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level.) version 3.0.8 installed on all systems as module MetaPhlAn3/3.0.8.
 

BioBakery (microbial community profiling) version 3.0 installed on all systems as module BioBakery/3.0.
It is a metapackage including: HUMAnN/3.0, KneadData/0.10.0, MetaPhlAn3/3.0.8 and
PhyloPhlAn/3.0.2

To use MELT software (Mobile Element Locator Tool), each potential user must agree to its software license. As a result, we cannot provide MELT through the module system, and have removed the MELT/2.0.2 and MELT/2.2.2 modules.  Each user that wishes to use MELT must agree to the MELT license and install the software for themselves.  Note that if the software is installed for a research group, each user in the research group must agree to the MELT license as well.

Salmon (a tool for wicked-fast transcript quantification from RNA-seq data) version 1.4.0 installed on all systems as module Salmon/1.4.0.

bonito (a PyTorch Basecaller for Oxford Nanopore Reads) version 0.3.8 for GPUs installed on snowy and bianca as module bonito/0.3.8.  Version 0.3.8 for CPUs only has been installed as module bonito/0.3.8-cpu on all systems.

All training models have also been downloaded for both, see 'module help bonito/0.3.8' or 'module help bonito/0.3.8-cpu' for more information.
 

unimap (fork of minimap2 optimized for assembly-to-reference alignment) version 0.1-r46-dirty installed on all systems as module unimap/0.1-r46-dirty.
 

minimap2 (versatile pairwise aligner for genomic and spliced nucleotide sequences) version 2.18-r1015 installed on all systems as module minimap2/2.18-r1015. In addition to minimap2, this installation provides the sdust too, the paftools.js tool for manipulating paf-format alignments, and the minimap2.py python wrapper.

k8 (Javascript shell based on Google's V8 Javascript engine which adds the support of flexible byte arrays and file I/O) version 0.2.5 installed on all systems as module k8/0.2.5.  k8 is designed for enabling Javascript as a general scripting language, rather than server-side operations. 
 

slurm-drmaa (DRMAA for Slurm: Implementation of the DRMAA C bindings for Slurm) version 1.1.2-slurm19.05.8 installed on all systems as module slurm-drmaa/1.1.2-slurm19.05.8.

NextPolish (fix base errors (SNV/Indel) in the genome generated by noisy long reads, it can be used with short read data only or long read data only or a combination of both) version 1.3.1 installed on all systems as module NextPolish/1.3.1.
 

jq (a lightweight and flexible command-line JSON processor) version 1.6 installed on all systems as module jq/1.6.

Tcl-Tk (Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches. Tk is the standard GUI for Tcl) version 8.6.11 installed on all systems as module Tcl-Tk/8.6.11.

FFmpeg (A complete, cross-platform solution to record, convert and stream audio and video) version 4.4 installed on all systems as module FFmpeg/4.4.

COIN-OR-OptimizationSuite (a collection of interoperable open source solvers from the respository of open source software maintained by the COIN-OR Foundation) version 1.8.0 installed on all systems as module COIN-OR-OptimizationSuite/1.8.0.
 

An omnibus collection of R packages for R/4.0.4 has been installed on all systems as module R_packages/4.0.4. There are a total of 20663 CRAN and BioConductor packages installed, out of 20751 packages available. 17354 CRAN packages are installed, out of 17428 available. 3309 BioConductor-specific packages are installed, out of 3323 available.

Some packages may require the loading of other modules to function correctly. For example, the Rmpi package requires loading openmpi/3.1.5 after loading R_packages/4.0.4. For more information, see 'module help R_packages/4.0.4'.

Yasm (Yasm is a complete rewrite of the NASM assembler under the 'new' BSD License) version 1.3.0 installed on all systems as module yasm/1.3.0.
 

GEOS (GEOS (Geometry Engine - Open Source) is a C++ port of the ​JTS Topology Suite (JTS). It aims to contain the complete functionality of JTS in C++. This includes all the ​OpenGIS Simple Features for SQL spatial predicate functions and spatial operators, as well as specific JTS enhanced functions. GEOS provides spatial functionality to many other projects and products.) version 3.9.1 compiled with gcc/9.3.0 is now installed on all systems as module GEOS/3.9.1-gcc9.3.0.
 

BOLT-LMM (software package currently consists of two main algorithms, the BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML algorithm for variance components analysis (i.e., partitioning of SNP-heritability and estimation of genetic correlations). ) version 2.3.5 installed on all systems as module BOLT-LMM/2.3.5.
 

HESS (HESS (Heritability Estimation from Summary Statistics) is a software package for estimating and visualizing local SNP-heritability and genetic covariance (correlation) from GWAS summary association data.) version 0.5.4-beta installed on all systems as module HESS/0.5.4-beta.
 

Open Babel (chemical toolbox designed to speak the many languages of chemical data, compiled with gcc 9.3.0) version 3.1.1-gcc9.3.0 installed on all systems as module openbabel/3.1.1-gcc9.3.0.
 

OpenBUGS (software package for performing Bayesian inference Using Gibbs Sampling) version 3.2.3 installed on all systems as module OpenBUGS/3.2.3.