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 3.8 installed on all systems as module HUMAnN/3.8.
 

MetaPhlAn4 (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 4.0 installed on all systems as module MetaPhlAn4/4.0.
 

Gurobi (The fastest and most powerful mathematical programming solver available for your LP, QP and MIP (MILP, MIQP, and MIQCP) problems.) version 10.0.2 installed on all systems as module Gurobi/10.0.2.

DATES ((Distribution of Ancestry Tracts of Evolutionary Signals) is a method to estimate the time of admixture in ancient DNA samples described in Chintalapati et al. 2022 biorxiv) version 4010 installed on all systems as module DATES/4010.
 

plink2 (association analysis toolset) version 2.00-alpha-5-20230923 installed on all systems as module plink2/2.00-alpha-5-20230923.
 

pbmm2 (pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments.) version 1.13.0 installed on all systems as module pbmm2/1.13.0.

MATLAB (a proprietary multi-paradigm programming language and numeric computing environment ) version R2023a installed on all systems as module matlab/R2023a.

paml (PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.) version 4.10.7 installed on all systems as module paml/4.10.7.
 

phyx (phyx performs phylogenetics analyses on trees and sequences) version 1.3 installed on all systems as module phyx/1.3. https://github.com/FePhyFoFum/phyx
 

The Python programming language version 3.11.4 plus a handful of widely used packages.

HyPhy (Open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.) version 2.5.51-mpi installed on all systems as module HyPhy/2.5.51-mpi.
 

HyPhy (Open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.) version 2.5.51 installed on all systems as module HyPhy/2.5.51.
 

InterProScan (InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites.) version 5.62-94.0 installed on all systems as module InterProScan/5.62-94.0.
 

Multi-CSAR (a scaffolding tool that can order and orient the contigs of a target draft genome based on multiple complete and/or incomplete reference genomes of related organisms) version 20180316-8fd582c installed on all systems as module Multi-CSAR/20180316-8fd582c.

Juicer (Juicer is a platform for analyzing kilobase resolution Hi-C data.) version 2.0 installed on all systems as module Juicer/2.0.
 

python_GIS_packages (Python package for GIS installation) version 3.10.8 installed on all systems as module python_GIS_packages/3.10.8.

Mathematica: high-powered computation with thousands of Wolfram Language functions, natural language input, real-world data, mobile support. https://www.wolfram.com/mathematica/

VarDictJava (a variant discovery program written in Java and Perl, a Java port of VarDict variant caller) version 1.8.3 installed on all systems as module VarDictJava/1.8.3.
 

WPS (WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs.) version 4.3.1 installed on all Rackham and Snowy as module WPS/4.3.1.
 

WRF (The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs.) version 4.3.0-dm-gcc installed on Rackham and Snowy as module WRF/4.3.0-dm-gcc.
 

snakemake (The Snakemake workflow management system is a tool to create reproducible and scalable data analyses) version 7.25.0 installed on all systems as module snakemake/7.25.0.
 

IRMA (Iterative Refinement Meta-Assembler. IRMA was designed for the robust assembly, variant calling, and phasing of highly variable RNA viruses.) version 1.0.3 installed on all systems as module IRMA/1.0.3.
 

XP-CLR (Code to compute xp-clr values as per Chen, Patterson & Reich 2010) version 1.1.2 installed on all systems as module XP-CLR/1.1.2.

dentist (Long sequencing reads allow increasing contiguity and completeness of fragmented, short-read based genome assemblies by closing assembly gaps, ideally at high accuracy.) version 4.0.0 installed on all systems as module dentist/4.0.0.

Moses is a statistical machine translation system that allows you to automatically train translation models for any language pair.

MEMEsuite (Motif-based sequence analysis tools) version 5.5.1 installed on all systems as module MEMEsuite/5.5.1.

PCAngsd (framework for analyzing low depth NGS data in heterogeneous populations using PCA) version 1.11 installed on all systems as module PCAngsd/1.11.

Cytoscape (A software platform for visualizing complex networks and integrating these with any type of attribute data.) version 3.9.1 installed on all systems as module Cytoscape/3.9.1.
 

VSCodium is a community-driven, freely-licensed binary distribution of Microsofts editor VS Code.

SLiM (An evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios.) version 4.0.1 installed on all systems as module SLiM/4.0.1.
 

gcta (analyses to better understand the genetic architecture of complex traits) version 1.94.1 installed on all systems as module gcta/1.94.1.
 

julia (Julia is a high-level, high-performance dynamic language for technical computing.) version 1.6.7_LTS installed on all systems as module julia/1.6.7_LTS.
 

julia (Julia is a high-level, high-performance dynamic language for technical computing) version 1.8.5 installed on all systems as module julia/1.8.5.
 

plink2 (association analysis toolset) version 2.00-alpha-3.7-20221024 installed on all systems as module plink2/2.00-alpha-3.7-20221024.
 

PROJ (Cartographic Projections and Coordinate Transformations Library) version 9.1.1 installed on all systems as module PROJ/9.1.1.
 

libtiff (This software provides support for the Tag Image File Format (TIFF), a widely used format for storing image data.) version 4.5.0 installed on all systems as module libtiff/4.5.0.
 

 delly (an integrated structural variant (SV) prediction method that can
  discover, genotype and visualize deletions, tandem duplications, inversions
  and translocations at single-nucleotide resolution in short-read and
  long-read massively parallel sequencing data) version 1.1.6 installed on
  all systems as module delly/1.1.6.

MMseqs2 (ultra fast and sensitive sequence search and clustering suite) version 14-7e284 installed on all systems as module MMseqs2/14-7e284.
 

HTSeq (Analysing high-throughput sequencing data with Python) version 2.0.2 installed on all systems as module htseq/2.0.2.

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 2.4.13c installed on all systems as module spaln/2.4.13c.
 

fastsimcoal (fast sequential markov coalescent simulation of genomic data under complex evolutionary models) version 2.7.93 installed on all systems as module fastsimcoal/2.7.93.
 

nf-core (A companion tool is available for nf-core to help with common tasks.) version 2.6 installed on all systems as module nf-core/2.6.
https://github.com/nf-core/tools

Nextflow (A DSL for data-driven computational pipelines http://nextflow.io) version 22.10.0 installed on all systems as module Nextflow/22.10.0.
https://github.com/nextflow-io/nextflow

abricate (mass screening of contigs for antimicrobial and virulence genes) version 1.0.1-20200512-955d402 installed on all systems as module abricate/1.0.1-20200512-955d402.
 

any2fasta (Convert various sequence formats to FASTA) version 0.4.2 installed on all systems as module any2fasta/0.4.2.
 

datamash (Datamash is a grouping and summarizing tool on tabular data files) version 1.8 installed on all systems as module datamash/1.8.

KrakenUniq (confident and fast metagenomics classification using unique k-mer counts) version 1.0.1 installed on all systems as module KrakenUniq/1.0.1.
 

pathPhynder (workflow for ancient DNA placement into reference phylogenies) version 1.a-20221011-a407a97 installed on all systems as module pathPhynder/1.a-20221011-a407a97.

fastq_screen_data (reference genomes for FastQ Screen, both standard and bisulfite) version 20220330 installed on all systems as module fastq_screen_data/latest. See 'module help fastq_screen_data/latest' for more information.

gsl (numerical library for C and C++ programmers) version 2.7 installed on all systems as module gsl/2.7.

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 3.11.0-gcc10.3.0 installed on all systems as module GEOS/3.11.0-gcc10.3.0.

KrakenUniq_data (latest database build for KrakenUniq, plus prebuilt databases available externally) version latest installed on all systems as module KrakenUniq_data/latest.  See 'module help KrakenUniq_data/latest' for more information.
 

fastq_screen (contamination screening for NGS data sets) version 0.15.2 installed on all systems as module fastq_screen/0.15.2.
 

VMD (molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting) version 1.9.3 installed on all systems as module VMD/1.9.3.
 

VMD (molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting) version 1.9.4-alpha-57 installed on all systems as module VMD/1.9.4-alpha-57.
 

KrakenUniq (confident and fast metagenomics classification using unique k-mer counts) version 1.0.0 installed on all systems as module KrakenUniq/1.0.0.
 

minimap2 (versatile pairwise aligner for genomic and spliced nucleotide sequences) version 2.24-r1122 installed on all systems as module minimap2/2.24-r1122.
 

[bio] vcfstats/0.4.2 installed on all systems

GeneMark (Gene prediction in eurkaryotes) version 4.69-es installed on all systems as module GeneMark/4.69-es.
 

phast (Phylogenetic Analysis with Space/Time models (PHAST) is a freely available software package consisting of a collection of command-line programs and supporting libraries for comparative and evolutionary genomics.) version 1.6 installed on all systems as module phast/1.6.
 

satsuma2 (optimised version of Satsuma, a tool to reliably align large and complex DNA sequences providing maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (to accomodate the billions of base pairs in vertebrate genomes).) version 37c5f38-20200304 installed on all systems as module satsuma2/37c5f38-20200304.
 

zlib (a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system) version 1.2.12 installed on all systems as module zlib/1.2.12.
 

bzip2 version 1.0.8 installed on all systems as module bzip2/1.0.8.
 

RStudio (Integrated development environment for the R language) version 2022.07.1-554 installed on all systems as module RStudio/2022.07.1-554.
 

xz (general-purpose data compression software with a high compression ratio) version 5.2.6 installed on all systems as module xz/5.2.6.
 

grenedalf is a collection of commands for working with population genetic data, in particular from pool sequencing. Its main focus are stat
istical analyses such as Tajima's D and Fst, following the approaches of PoPoolation and PoPoolation2)

version 0.2.0-beta installed on all systems as
module grenedalf/0.2.0-beta
 

libcurl (a free and easy-to-use client-side URL transfer library supporting many formats) version 7.85.0 installed on all systems as module libcurl/7.85.0.
 

texlive (full TeX document production system) version 2022-09-18 installed on all systems as module texlive/2022-09-18.
 

zstd (a fast lossless compression algorithm, targeting real-time compression scenarios at zlib-level and better compression ratios) version 1.5.2 installed on all systems as module zstd/1.5.2.

octopus (Mapping-based variant caller that implements several calling models within a unified haplotype-aware framework) version 17a597d-20220708 installed on all systems as module octopus/17a597d-20220708.
 

MAGeCK2 (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) version 20211209-435eacd installed on all systems as module MAGeCK2/20211209-435eacd.
 

MAPGD (MAPGD is a series of related programs that estimate allele frequency, heterozygosity, Hardy-Weinberg disequilibrium, linkage disequilibrium and identity-by-descent (IBD) coefficients from population genomic data using a statistically rigor
ous maximum likelihood approach.)

https://github.com/LynchLab/MAPGD
 

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