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.
 

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 installed on all systems as module MetaPhlAn3/3.0.

SLiM (An evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios.) version 3.6 installed on all systems as module SLiM/3.6.

ROOT (modular scientific software toolkit. It provides all the functionalities needed to deal with big data processing, statistical analysis, visualisation and storage) version 6.22.08 installed on all systems as module ROOT/6.22.08.
 

ImageMagick (create, edit, compose, or convert digital images) version 7.0.11-3 installed on all systems as module ImageMagick/7.0.11-3.
 

MultiQC (Aggregate results from bioinformatics analyses across many samples into a single report) version 1.10.1 installed on all systems as module MultiQC/1.10.1.
 

GhostPDL (interpreters for page description languages PS, PDF, XPS, PCL) version 9.53.3 installed on all systems as module GhostPDL/9.53.3.  This includes the well-known Ghostscript interpreter, and also includes header files and the shared library libgs.so.

HaplotypeReferenceConsortium (The Haplotype Reference Consortium (HRC) will create a large reference panel of human haplotypes by combining together sequencing data from multiple cohorts) version r1.1 installed on all systems as module HaplotypeReferenceConsortium/r1.1.
 

MaSuRCA (The MaSuRCA (Maryland Super Read Cabog Assembler) genome assembly and analysis toolkit contains of MaSuRCA genome assembler, QuORUM error corrector for Illumina data, POLCA genome polishing software, Chromosome scaffolder, jellyfish mer counter, and MUMmer aligner.) version 4.0.2 installed on all systems as module MaSuRCA/4.0.2.

Pilon (Pilon is a software tool which can be used to: Automatically improve draft assemblies & Find variation among strains, including large event detection) version 1.24 installed on all systems as module Pilon/1.24.
 

NPStat (Population genetics tests and estimators for pooled NGS data) version 1 installed on all systems as module NPStat/1.
 

MELT (The Mobile Element Locator Tool (MELT) is a software package, written in Java, that discovers, annotates, and genotypes non-reference Mobile Element Insertions (MEIs) in Illumina DNA paired-end whole genome sequencing (WGS) data. ) version 2.2.2 installed on all systems as module MELT/2.2.2.
 

DANPOS (A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing) version 3.1.1 installed on all systems as module DANPOS/3.1.1. Also, version 2.2.2 installed on all systems as module DANPOS/2.2.2.

bcftools, htslib and samtools (tools for working with SAM/BAM/CRAM format files and variant files) version 1.12 installed on all systems as module bcftools/1.12, htslib/1.12 and samtools/1.12.

Roary (Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome) version 3.13.0 installed on all systems as module Roary/3.13.0.
http://sanger-pathogens.github.io/Roary/

gmap-gsnap (Genomic Mapping and Alignment Program for mRNA and EST Sequences) version 2021-03-08 installed on all systems as module gmap-gsnap/2021-03-08.
 

Protocol Buffers (a.k.a., protobuf) are Google's language-neutral, platform-neutral, extensible mechanism for serializing structured data.  Version 3.15.5 is installed in two modules: protobuf/3.15.5 is compiled with the system gcc, at installation this is version 4.8.5; and protobuf/3.15.5-gcc9.3.0 is compiled with module gcc/9.3.0.
 

Rcorrector (Rcorrector(RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.) version 1.0.4 installed on all systems as module Rcorrector/1.0.4.
 

beast2 (Bayesian Evolutionary Analysis by Sampling Trees) version 2.6.3 installed on all systems as module beast2/2.6.3.  All packages as available 2021-03-08 are also installed.

libsodium (Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.) version 1.0.18-stable installed on all systems as module libsodium/1.0.18-stable.
 

libzmq (the ZeroMQ lightweight messaging kernel is a library which extends the standard socket interfaces with features traditionally provided by specialised messaging middleware products. ZeroMQ sockets provide an abstraction of asynchronous message queues, multiple messaging patterns, message filtering (subscriptions), seamless access to multiple transport protocols and more.) version 4.3.4 installed on all systems as module libzmq/4.3.4.
 

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.