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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

deal.II (open source finite element library) version 9.1.1 is now installed as two modules on all systems: deal.II/9.1.1-gcc, built with GCC 8.2.0 and OpenMPI 3.1.3; and deal.II/9.1.1-intel, build with Intel compilers 2019.1.144, Intel MPI 2018.4.274, and GCC 8.2.0.

These modules are built using EasyBuild with the foss/2019a and the intel/2019a toolchains, respectively.  For more information, see 'module help deal.II/9.1.1-gcc and 'module help deal.II/9.1.1-intel'.

NanoComp (compare multiple runs of long read sequencing data and alignments) version 1.9.2 is now installed as module NanoComp/1.9.2 on all systems.

MultiQC (comprehensive log file summariser) version 1.8 is now installed as module MultiQC/1.8 on all systems.

FastANI (fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)) version 1.2 installed on all systems as module FastANI/1.2.

LDpred (software package that adjusts GWAS summary statistics for the effects of linkage disequilibrium) version 1.0.8 is now installed as module LDpred/1.0.8 on all systems.

Stacks (Software pipeline for building loci from short-read sequences) version 2.41 installed on all systems as module Stacks/2.41.

QCTOOL (manipulation and quality control of GWAS datasets and other genome-wide data) version 2.0.6 is installed as module qctool/2.0.6 on all systems.

Metaxa2 (Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data) version 2.2 is newly installed on all systems as module Metaxa2/2.2, and version 2.1.3, previously available on milou, is now available on all systems as module Metaxa2/2.1.3.

GOTM (general ocean turbulence model) version 5.3-221-gac7ec88d is now installed as module GOTM/5.3-221-gac7ec88d on all systems.

CDO (large tool set for working on climate and NWP model data) version 1.9.5 is now installed as module CDO/1.9.5 on all systems.

usearch (versatile tool for metagenomics) version 11.0.667 installed on all systems as module usearch/11.0.667.

vsearch (Versatile open source tool for metagenomics) version 2.14.1 installed on all systems as module vsearch/2.14.1.

The latest development version of BCFTools has been installed as bcftools/1.9-develop on all systems.  This also uses the latest development version of HTSlib.  This development version provides the +split-vep plugin and perhaps has other features, but its use comes with some risk: some of the tests for the +fill-tags plugin fail, and there may be other bugs as well.  Use with these cautions in mind.

ALPS (Algorithms and Libraries for Physics Simulations) is an open source effort aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as C++ libraries for simplifying the development of such code.  Version 2.3.0 has been installed as module ALPS/2.3.0 on all systems.  When loading the module the ALPS system will be available to use but not build against; see 'module help ALPS/2.3.0' for instructions on steps to follow so that this module can be built against.

Diamond (Fast blast replacement for protein alignments) version 0.9.26 installed on all systems as module diamond/0.9.26.

Graphviz (Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks.) version 2.40.1 installed on all systems as module Graphviz/2.40.1.

Maker (portable and easily configurable genome annotation pipeline) version 2.31.10 is now installed as module maker/2.31.10 on all systems.  This is built with MPI support by default.

Pysam (Python API for handling SAM and BAM files) version 0.15.3 is now available for two python module versions: pysam/0.15.3-python3.6.8 and pysam/0.15.3-python3.7.2.

fcGENE (Format converting tool for genotype Data (e.g.PLINK-MACH,MACH-PLINK)) version 1.0.7 installed on all systems as module fcGENE/1.0.7.

Kaiju (fast and sensitive taxonomic classification for metagenomics) version 1.7.2 has been installed as module kaiju/1.7.2 on all systems.

Slurm received a major update during the October maintenance stop. Check out these slides to learn about some of the changes that may impact you!

BraCeR (BraCeR - reconstruction of B cell receptor sequences from single-cell RNAseq data) version 2019_10_03_22e49cb installed on all systems as module BraCeR/2019_10_03_22e49cb.
 

UPPMAX-local Blast (canonical sequence search tool) version 2.9.0+ is now installed as module blast/2.9.0+ on all Uppmax systems.  This is the first blast module version to support the V5 databases now provided by NCBI.  Currently available are nr_v5, nt_v5, refseq_protein_v5 and refseq_rna_v5.  These databases include taxonomy information and other features.  NCBI will discontinue updating the older database versions at the end of September 2019.

Velocyto (library for the analysis of RNA velocity) version 0.17.17 is now installed as module velocyto/0.17.17 on all systems.

pblat (threads-enabled version of the blat aligner) version 2.1 and pblat-cluster (MPI-enabled version of blat) version 1.0 are now installed on all clusters as pblat/2.1 and pblat-cluster/1.0 , respectively.  Each is updated to blat v36x2 (jksrc.v376).

FASTA (search protein and DNA sequence databases, and to confirm the statistical significance of a match by comparing the alignment score to a distribution of scores produced by shuffled sequences) version 36.3.8h, together with versions 36.3.6d, 36.3.6f, 36.3.8, are now installed as module fasta/36.3.8h and corresponding modules on all systems.

R (statistical system) version 3.6.1 and the corresponding R_packages module are now installed on all systems.  The R_packages/3.6.1 module contains a total of 17657 CRAN and BioConductor packages installed, out of 17992 packages available.  Of these, 14579 CRAN packages are installed, out of 14913 available, and 3054 BioConductor-specific packages are installed, out of 3079 available.

STAR-Fusion (fusion transcript detection) version 1.7.0 is now installed as module star-fusion/1.7.0 on all systems.  This version requires and loads as a prerequisite the star/2.7.2b module, which contains new features upon which star-fusion/1.7.0 is dependent.  Local copies of the CTAT Genome Resource Libraries are currently being updated; see 'module help star-fusion/1.7.0' for more information.

CDO (collection of command line Operators to manipulate and analyse climate and NWP model data) version 1.9.7.1 is now installed as modules CDO/1.9.7.1, compiled with and using prerequisites compiled with the system gcc, and CDO/1.8.7.1-intel18.3, compiled with and using prerequisites compiled with the intel/18.3 compiler.

Magics (meteorological plotting software) version 3.3.1 is now installed as modules Magics/3.3.1, compiled with the system gcc, and Magics/3.3.1-intel18.3, compiled with the intel/18.3 compiler.

The ecCodes library (encoding and decoding of meteorological messages in various formats) version 2.13.1 is now installed as module ecCodes/2.13.1 on all systems.

PROJ.4 (geographical information library) version 4.9.3 has been installed as module PROJ.4/4.9.3, compiled with system gcc, and PROJ.4/4.9.3-intel18.3, compiled with the intel/18.3 compiler.

The HDF5 library version 1.10.5 has been installed on all systems as module hdf5/1.10.5, compiled with system gcc, and hdf5/1.10.5-threadsafe-intel18.3, compiled with the threadsafe option and the intel/18.3 compiler.  These modules make use of compression provided by szip/2.1.1 and zlib/1.2.11, which are loaded as prerequisites.

STAR aligner (Spliced Transcripts Alignment to a Reference) version 2.7.2b is now installed as module star/2.7.2b on all systems.

GEM-Tools (together with the bundled GEM library are a set of very optimized tools for indexing and querying huge genomes and files, and tools to make these easier to use) version 1.7.1 is now installed as module GEM-Tools/1.7.1 on all systems.

GEM (high resolution peak calling and motif discovery for ChIP-seq and ChIP-exo data) version 3.4 is now installed on all systems, and version 2.7 (previously installed on milou) is also made available on all systems.

ExaBayes (Software package for Bayesian tree inference, particularly suitable for large-scale analyses on computer clusters) version 1.5 is now installed as module ExaBayes/1.5, with single-node multithread support, and ExaBayes/1.5-mpi, with multi-node multithread support.  Refer to 'module help ExaBayes' for assistance on using ExaBayes.

The SPAdes assembler version 3.13.1 is now installed as module spades/3.13.1 on all systems.

The NetCDF library version 4.7.1 has been installed as module netcdf/4.7.1, compiled with system gcc, and netcdf/4.7.1-intel18.3, compiled with the intel/18.3 compiler.  This makes use of the hdf5/1.10.5 and hdf5/1.10.5-intel18.3 libraries, respectively.

The FreeType type management library version 2.10.1 is now installed as module freetype/2.10.1 on all systems.

rtgtools version 3.10.1 installed on all systems, RTG Tools is a subset of RTG Core that includes several useful utilities for dealing with VCF files and sequence data. Probably the most interesting is the vcfeval command which performs sophisticated comparison of VCF files.

ART (ART is a set of simulation tools to generate synthetic next-generation sequencing reads.) version 2016-06-05 installed on all systems as module ART/2016-06-05.

https://www.niehs.nih.gov/research/resources/software/biostatistics/art/

VerifyBamID2 (robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method) version 1.0.6 is installed as module VerifyBamID2/1.0.5 on all systems.

verifyBamID (verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples) version 1.1.3 is now installed as module verifyBamID/1.1.3 on all systems.

The latest version of the Amazon Web Services Command-Line Interface has been installed as module awscli/1.16.225 on all systems.

Blobtools (modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets) version 1.1.1 is now installed as module blobtools/1.1.1 on all systems.  See 'module help blobtools/1.1.1' for advice on building your own taxonomy database.

Circos (software package that visualizes data in a circular layout) version 0.69-9 is now installed as module circos/0.69-9 on all systems.

The latest version of IQ-TREE (efficient phylogeny estimation) has been installed as module iqtree/1.6.12-omp-mpi on all systems.  To use the MPI-enabled versions, it is necessary to load the gcc/8.2.0 and openmpi/3.1.1 modules; see 'module help iqtree/1.6.12-omp-mpi' for more information.

An error in a module file prevented the longranger/2.2.2 module from working correctly.  This is now fixed.

Boost (free peer-reviewed portable C++ source libraries) version 1.70.0 has been provided compiled with different combinations of GCC and Intel compilers, with and without MPI.  The name of each module version reflects the compiler(s) used to compile that version but those are not loaded when the boost module is loaded; that is left for the user to decide.  Now installed as modules on all systems are boost/1.70.0_gcc9.1.0, boost/1.70.0_gcc9.1.0_mpi3.1.3, boost/1.70.0_intel18.3, and boost/1.70.0_intel18.3_mpi3.1.3.

bgen (Reference implementation of the BGEN format) version 1.1.4 installed on all systems as module bgen/1.1.4.

DOCK version 3.7 installed on all systems as module DOCK/3.7.
http://dock.compbio.ucsf.edu/DOCK_3.7/

HiCUP (a tool for mapping and performing quality control on Hi-C data) version 0.7.2 installed on all systems as module HiCUP/0.7.2.

Transrate (software for transcriptome assembly analysis) versions 1.0.1 and 1.0.2 are now installed as modules transrate/1.0.1 and transrate/1.0.2 on all systems.  It appears that transrate/1.0.3 has bugs; it is not clear whether this extends to transrate/1.0.2. It is recommended to use transrate/1.0.1.

HyPhy (hypothesis testing using phylogenies) version 2.5.0 is now installed as module HyPhy/2.5.0 (for single-node use, with threads support) and HyPhy/2.5.0-mpi (for multinode use, with MPI support).

STAR (spliced RNA-seq aligner) version 2.7.1a is now installed as module star/2.7.1a on all systems.

FusionCatcher (finds somatic fusion genes in RNA-seq data) version 1.10 is now installed as module FusionCatcher/1.10 on all systems.  See 'module help FusionCatcher/1.10' for more information.

Bowtie (older-tech but still widely used short-read aligner) versions 1.2.2 and 1.2.3 are now installed as modules bowtie/1.2.2 and bowtie/1.2.3 on all systems.

Picard tools (various tools for manipulating bioinformatics files) versions 2.19.2 and 2.20.4 are now installed as modules picard/2.19.2 and picard/2.20.4, respectively.

BBMap (short-read aligner and other tools) version 38.61b is installed as module bbmap/38.61b on all systems.

STAR (splice-aware RNA-seq aligner) version 2.7.0f is now installed as module star/2.7.0f on all systems.

Blat (general-purpose aligner) verison 36 is now available as module blat/36 on all systems.

Four older versions of BWA (read aligner) not available since kalkyl or milou are now available on all systems: bwa/0.5.8a, bwa/0.5.9, bwa/0.6.1, bwa/0.6.2

SortMeRNA (next-generation sequence filtering and alignment tool) version 3.0.3 is now installed as module SortMeRNA/3.0.3 on all systems.  Also included are indexed RNA databases, and the auxiliary scripts are now available in the path; see 'module help SortMeRNA/3.0.3' for more information.

DosageConvertor (a C++ tool to convert dosage files (in VCF format) from Minimac3/4 to other formats such as MaCH or PLINK) version 1.0.4 installed on all systems as module DosageConvertor/1.0.4.

SiBELia (comparative genomics tool that assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments) version 3.0.7 is now installed as module SiBELia/3.0.7 on all systems.

SMARTdenovo (de novo long-read assembly) through commit 5cc1356 on 19 Feb 2018 is now installed as module SMARTdenovo/20180219-5cc1356 on all systems.

Wtdbg2 (de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies) version 2.4 is now installed as module wtdbg2/2.4 on all systems.

Flye (de novo assembler for single molecule sequencing reads) version 2.4.2 is now installed as module Flye/2.4.2 on all systems.

Filtlong (tool for filtering long reads by quality) version 0.2.0 through commit 13504b7 on 15 May 2019 is now installed as module Filtlong/0.2.0-20190515-13504b7 on all systems.

Porechop (tool for finding and removing adapters from Oxford Nanopore reads) is now installed as module Porechop/0.2.4 on all systems.

The SRA Toolkit (tools for interacting with NCBI's Short Read Archive) version 2.9.6 has been installed as module sratools/2.9.6-1 on all systems.

Canu (single-molecule assembly, a fork of the original Celera Assembler) version 1.8 is now installed as module canu/1.8 on all systems.

Gnuplot (general purpose plotting tool) version 5.2.7 is now installed as module gnuplot/5.2.7 on all systems.

BioPerl (Perl toolkit for working with bioinformatic data) version 1.7.2 for perl version 5.26.2 is now installed as module BioPerl/1.7.2_Perl5.26.2 on all systems.

PhyML (Phylogenetic estimation using (Maximum) Likelihood) version 3.3.20190321 has been installed as module PhyML/3.3.20190321 on all systems.  The tools phyml, phyrex and phytime are available.

Several bioinformatics modules that were previously available on Milou or on a subset of current systems are now available on all systems: rdp-classifier/2.2, rdp-classifier/2.4, Roary/3.6.2, QuorUM/1.0.0, RDXplorer/3.2.  If you require any other modules not currently available on active systems that were previously available on Milou, please let us know.