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.

RegScan (fast association analysis between allele frequencies and continuous traits. It uses linear regression to estimate marker effects on continuous traits) version 0.5 is now installed as module RegScan/0.5 on all systems.  Please give it a couple of days to propogate to all compute nodes, as there is a system library that needs to be installed for it to work everywhere.

Perl 6 (advanced scripting language) version Rakudo Star 2019.03 is now installed as module perl6/rakudo-star-2019.03 on all systems.

The Julia programming language version 1.1.1 is now installed as module julia/1.1.1 on all systems.

SMRT Link (analysis software for PacBio long-read technology) version 7.0.1 has been installed on all systems as module SMRT/7.0.1.

Git (free and open source distributed version control system) version 2.21.0 is now installed as module git/2.21.0 on all systems.

Bowtie2 (ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences) version 2.3.5.1 has been installed as module bowtie2/2.3.5.1 on all systems.

Bismark ((tool to map bisulfite converted sequence reads and determine cytosine methylation states) version 0.22.1 installed on all systems as module bismark/0.22.1 on all systems.

Chromium Long Ranger (set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants) version 2.2.2 is now installed on all systems as module longranger/2.2.2.

RAxML-NG (phylogenetic tree inference tool which uses maximum-likelihood optimality criterion) version 0.9.0 has been installed as module RAxML-NG/0.9.0 (single-node runs) and MPI-enabled as module RAxML-NG/0.9.0-mpi, which supports running on multiple nodes.

Yleaf (Detection of Y-Haplogroups in Human genome DNA) version 2.0 installed on all systems as module Yleaf/2.0.  Indices for both hg19 and hg38 are available.

medaka (A tool to create a consensus sequence from nanopore sequencing data) version 0.7.1 installed on all systems as module medaka/0.7.1.
 

Oncotator (A tool for annotating human genomic point mutations and indels with data relevant to cancer researchers.) version 1.9.9.0 installed on all systems as module oncotator/1.9.9.0.

Kraken2 (second version of the Kraken taxonomic sequence classification system.) version 2.0.8-beta installed on all systems as module Kraken2/2.0.8-beta.

PSMC (Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model) version 0.6.5-r67-e5f7df5 (version 0.6.5-r67 with additional changes, see website) installed on all systems as module psmc/0.6.5-r67-e5f7df5.

GEMMA (Software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets.) version 0.98.1 installed on all systems as module GEMMA/0.98.1.

Kallisto (quantifying abundances of transcripts from bulk and single-cell RNA-Seq data) version 0.45.1 is now installed as module kallisto/0.45.1 on all systems.

Exonerate (protein alignment and utilities) version 2.4.0 is now installed as module exonerate/2.4.0 on all systems.

R (statistical language and environment) version 3.6.0 "Planting of a Tree" is now installed as module R/3.6.0 on all systems.  The R_packages/3.6.0 module has also been updated and now contains 16800 CRAN and BioConductor packages.

DeepVariant (An analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.) version 0.8.0 installed on all systems as module DeepVariant/0.8.0.

Diamond (accelerated BLAST compatible local sequence aligner) version 0.9.24 is now available as module diamond/0.9.24 on all systems.

snakemake version 5.4.5 installed on all systems as module snakemake/5.4.5.

Trim Galore! (wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files) version 0.6.1 is now installed as module TrimGalore/0.6.1 on all systems.

FastQC (sequence quality tools) version 0.11.8 is now installed as module FastQC/0.11.8 on all systems.

Cutadapt (flexible adapter trimming) version 2.3 is now installed as module cutadapt/2.3 on all systems.

Redundans (pipeline that assists an assembly of heterozygous/polymorphic genomes, including de novo assembly) version 0.14a, branch de_novo, as of the latest commit 42e8edf on 2019-03-14, has been installed as module Redundans/0.14a-de_novo-42e8edf-20190314 on all systems.  This is a development project and may contain bugs, use Redundans/0.14a-d11d32b-20190313 unless you know what you are doing.  See 'module help Redundans/0.14a-de_novo-42e8edf-20190314' for more information.

Redundans (pipeline that assists an assembly of heterozygous/polymorphic genomes) version 0.14a and following commits up to d11d32b on 2019-03-13, is now installed as module Redundans/0.14a-d11d32b-20190313 on all systems.

Platanus-allee (assembler that attempts to assemble separate homologous chromosomes in highly heterozygous species) version 2.0.2 is now installed as module Platanus-allee/2.0.2 on all systems.

Platanus (high-throughput assembler that can handle highly heterozygous genomes) version 1.2.4 is now installed as module Platanus/1.2.4 on all systems.  The version 1.2.1 previously available on milou is also now installed for all current clusters.

Minimap2 (versatile pairwise aligner) version 2.16 is now installed as module minimap2/2.16 on all systems.

Stargazer (a bioinformatics tool for calling star alleles in various polymorphic pharmacogenes from next-generation sequencing (NGS) data.) version 1.0.4 installed on all systems as module Stargazer/1.0.4.

LTR_Finder (efficient program for finding full-length LTR retrotranspsons in genome sequences) version 1.0.7 is available as module LTR_Finder/1.0.7 on all systems.  GtRNAdb databases are available, see 'module help LTR_Finder/1.0.7' for more information.  When on milou, this module was named 'ltr-finder'.

Gromacs versions 2019.1 and 2018.6 compiled with -DGMX_THREAD_MPI=ON -DGMX_OPENMP=ON are availabe on Rackham.

• gromacs/2019.1.th
• gromacs/2018.6.th

GATK (variant calling and more) versions 4.1.0.0 and 4.1.1.0 are now installed as modules GATK/4.1.0.0 and GATK/4.1.1.0 on all systems.  The gatk wrapper available for each makes it easy to run each; see 'module help GATK/4.1.1.0' for more information.

The p7zip/16.02 module has been repaired, by adding additional executables 7z and 7zr.

Version 5.1.0 of GNU Octave, a Matlab-compatible programming language for scientific computing,  is now available on all systems as module octave/5.1.0.

UMI-tools (tools for dealing with Unique Molecular Identifiers) version 1.0.0 was published as module umi_tools/1.0.0.

STAR-fusion (use the STAR aligner to identify candidate fusion transcripts supported by Illumina reads) version 1.5.0 is now installed as module star-fusion/1.5.0 on all systems.  Also installed and newly available are the genome resource libraries both for version 1.5.0 and earlier versions of star-fusion.  See 'module help star-fusion/1.5.0' for more information.

PRINSEQ (sequence data quality control and preprocessing) version 0.20.4 is installed as module prinseq/0.24.1 on all systems.

OpenFOAM 4.1 is now installed on Rackham.

module load OpenFOAM/4.1

source $FOAM_BASHRC

Should you wish to use it together with the waves2Foam tool:

module load OpenFOAM/4.1-waves2Foam

source $FOAM_BASHRC

Please unload all modules (except for the uppmax one) prior to loading OpenFOAM.

Gromacs versions 2019.1, 2018.6, and 2016.6 are available as modules on Rackham: 

• gromacs/2019.1
• gromacs/2018.6
• gromacs/2016.6

The cairo libraries (2D graphics plotting) version 1.17.2 are now installed as module cairo/1.17.2 on all systems.

VIM (text editor and more) version 8.1-1053 is now installed as module vim/8.1-1053 on all systems.  Included is scripting support for python/2.7.15, python3/3.7.2, ruby/2.6.2, perl, and tcl.

Ruby (programming language) version 2.6.2 is now installed as ruby/2.6.2 on all systems.  Both shared and static versions of libruby are also provided.

STAR (Spliced Transcripts Alignment to a Reference) version 2.7.0e is now installed as module star/2.7.0e on all systems.  The 2.7.0 released include support for STARsolo, single-cell alignments that are said to be ~10x faster than CellRanger.

Phast (phylogenetic analysis with space/time models) version 1.5 is now installed as module phast/1.5 on all systems.

Apache Maven (software project management and comprehension tool) version 3.6.0 has been installed as module maven/3.6.0 as part of build-tools on all systems.

Gnu automake (build configuration) version 1.16.1 is installed as module automake/1.16.1 on all systems.

RStudio (integrated development environment for R statistical language) version 1.1.463 is now installed as module RStudio/1.1.463 on all systems.

SNPTEST (analysis of single SNP association in genome-wide studies) version 2.5.5 has been installed as module SNPTEST/2.5.5 on all systems.

QCTOOL (command-line utility program for manipulation and quality control of gwas datasets and other genome-wide data) version 2.0.1 is now installed as module qctool/2.0.1 on all systems.

FineSTRUCTURE (fast and powerful algorithm for identifying population structure using dense sequencing data) version 4.0.1 is now installed as module fineSTRUCTURE/4.0.1 on all systems.  See 'module help fineSTRUCTURE/4.0.1' for more information.

Python version 3.7.2 is now installed as module python/3.7.2 on all systems.  Several packages are included with this installation, including up-to-date versions of pip, setuptools, wheel, Cython, numpy, scipy, matplotlib, PyYAML, pandas, h5py, twisted, requests, nltk, pillow, pygments, ipython, jupyter, virtualenv, gitpython, and graphviz.

IQ-TREE (efficient software for phylogenomic inference) version 1.6.10 is now installed as module iqtree/1.6.10-omp-mpi.  Several different executables with different multithreading capabilities are available; see 'module help iqtree/1.6.10-omp-mpi' for more information.

EggNOG mapper (fast genome-wide functional annotation through orthology assignment) version 1.0.3 is now installed as module eggNOG-mapper/1.0.3.  The EggNOG databases version 4.5.1 are also installed for local use; see 'module help eggNOG-mapper/1.0.3' for more information.

SURVIVOR (Tools for Structural Variations in the VCF format) version 1.0.3,

is a tool set for simulating/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs, is now installed on all systems as module SURVIVOR/1.0.3.

Python version 3.6.8 (last bugfix release of python3.6) is now installed as module python/3.6.8 on all systems.  Several packages are included with this installation, including up-to-date versions of pip, setuptools, wheel, Cython, numpy, scipy, matplotlib, PyYAML, pandas, h5py, twisted, requests, nltk, pillow, pygments, ipython, jupyter, virtualenv, gitpython, and graphviz.

Phyutility (simple analyses and modifications of trees and data matrices on the command line) version 2.7.3 is now installed as phyutility/2.7.3 on all systems.

SLiM (evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios) version 3.2.1 is now installed as module SLiM/3.2.1 as part of bioinfo-tools on all systems.

Blasr (PacBio's own long read aligner) version 5.3.2 is now installed as module blasr/5.3.2 on all systems.

Cutadapt (finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from high-throughput sequencing reads) version 2.0 is now installed as module cutadapt/2.0 on all systems.

RGT (A python library and set of tools  for the integrative analysis of  high throughput regulatory genomics data) version 0.11.6 installed on all systems as module RGT/0.11.6

The meson build system version 0.49.2 is now installed as module meson/0.49.2 as part of the build-tools subgroup of modules.

The Ninja build system version 1.9.0 has been installed as module ninja/1.9.0 as part of the build-tools subgroup of modules on all systems.

LoRDEC (correcting sequencing errors in long reads such as PacBio and Oxford Nanopore using highly accurate short reads such as Illumina) version 0.9 is now installed as module LoRDEC/0.9 on all systems.

Nibabel version 2.3.3 installed on all systems as module nibabel/2.3.3.

An updated GATK resource bundle from Broad Institute has been installed at /sw/data/uppnex/GATK/.

BioPython 1.73 has been installed on all systems.  The module biopython/1.73 is installed with and uses python/2.7.15, and biopython/1.73-py3 is installed with and uses python/3.6.0.

CheckM (tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes) 1.0.12 is now installed as CheckM/1.0.12 on all systems.  Also installed and configured are the CheckM data files.

[bio] Drosophila melanogaster genomes (dm3, dm6) installed for ngsplot.

The Wolfram Mathematica program has been installed on Rackham and Snowy as module mathematica/11.2. We have no generally available license for this software, please turn to your local license responsible and ask for network licenses.

R (statistical analysis system) version 3.5.2 and the corresponding omnibus module containing R packages, R_packages/3.5.2, are now installed on all systems.  R_packages/3.5.2 contains 13355 CRAN packages installed, out of 13683 available, and 2933 BioConductor-specific packages installed, out of 2959 available. 

ANNOVAR (variant annotation) version 2018.04.06 has been installed as module annovar/2018.04.16 on all systems.

PILER-64 (identification and classification of genomic repeats) version 1.0 is now installed as module PILER-64/1.0 on all systems.  This is a 64-bit large-memory version of the original PILER (http://www.drive5.com/piler/piler_userguide.html), and thus suitable for finding repeats in large, complex genomes.

TRF (tandem repeats finder) version 4.09 is installed as module trf/4.09 on all systems.  The legacy version trf/4.07b is now also available on all systems.

RepeatModeler (de-novo repeat family identification and modeling package)1.0.11 is now installed as module RepeatModeler/1.0.11 on all systems.  Several auxiliary programs are provided; see 'module help RepeatModeler/1.0.11' for more details.

RepeatMasker version 4.0.8 (screen DNA sequences for interspersed repeats and low complexity DNA sequences) has been installed as module RepeatMasker/4.0.8 on all systems.  This includes RMBlastn 2.6.0+, hmmer, cross_match, trf, nseg, as well as RepBase RepeatMasker edition 20181026, Dfam 2.0 and Dfam_consensus 20171107.

ANTs (Advanced Normalization Tools for biomedical images) version 2.3.1 is now installed as module ANTs/2.3.1 on all clusters.

CMake (build configuration and automation tool) version 3.13.2 is now installed as cmake/3.13.2 on Uppmax clusters.

Stacks 2.2 (software pipeline for building loci from short-read sequences such as RAD-Seq) is installed as module Stacks/2.2 on all systems.

MultiQC version 1.7 (results aggregator for bioinformatic analyses) is now installed as module MultiQC/1.7 on all systems.

10X Chromium Cell Ranger version 3.0.1 (single-cell RNA-Seq; works with the latest 10X chemistry) is now installed as module cellranger/3.0.1 on all systems.

The latest version of Cell Ranger data (3.0.0) is also installed.  See 'module help cellranger/3.0.1' for more information.

GMAP-GSNAP version 2018-07-04 (alignment of transcripts and short reads) is isntalled as gmap-gsnap/2018-07-04 on all Uppmax systems. 

The R packages rrbgen version 0.0.6 (read and write BGEN SNP files) and STITCH version 1.5.4 (haplotype imputation) have been installed as part of the existing R_packages/3.5.0 module, and will be included in future versions of the R_packages module.

Bowtie2 (short read aligner) version 2.3.4.3 has been installed as module bowtie2/2.3.4.3 on all systems.

The URL used by the chipster/webstart module has been updated to use https.  The use of chipster via this module still requires an account at https://chipster.csc.fi/, and it will request account credentials when started.

HiCExplorer (a set of tools to process, normalize and visualize Hi-C data) version 2.2-beta installed as module HiCExporer/2.2-beta on all systems.

TIDDIT (Tool to identify chromosomal rearrangements using Mate Pair or Paired End sequencing data.) version 2.3.0 was installed as module TIDDIT/2.3.0 on all systems

Minimac4 (an efficient implementation of the genotype imputation algorithms in minimac/mininac2/minimac3) version 1.0.0 installed as module Minimac4/1.0.0 on all systems

Tigmint (assembly correction via linked reads) version 1.1.2 is now installed as module tigmint/1.1.2 on all Uppmax systems.

MUMmer4 version 4.0.0beta2 is now installed as MUMmer/4.0.0beta2 on all systems.

Qiime2 (next-generation microbiome bioinformatics platform) version 2018.11.0 installed as module qiime2/2018.11.0 on all systems

MaxBin (clustering metagenomic contigs into different bins, each consists of contigs from one species) version 2.2.5 was install as module MaxBin/2.2.5 on all systems.

CONCOCT (program for unsupervised binning of metagenomic contigs) development version 0.5.0 installed as module CONCOCT/0.5.0 on all systems

albacore (data processing pipeline that provides the Oxford Nanopore basecalling algorithms, and several post-processing steps.) build 4aee41d installed as module albacore/4aee41d on all systems.

LASER (estimate individual ancestry for sequencing reads) 2.04 is now installed as module LASER/2.04 on all systems.  The earlier versions LASER/2.01 and LASER/2.02 were also provided for all systems.

RAxML-NG (next-generation phylogenetic inference) version 0.7.0 Beta has been installed without and with MPI support, as module versions RAxML-NG/0.7.0b and RAxML-NG/0.7.0b-mpi, respectively.

MACS (tool for identifying transcript factor binding sites) version 2.1.2 was installed as module MACS/2.1.2 on all systems

hichipper (data processing and quality control pipeline for HiChIP data) version 0.7.3 was installed as module hichipper/0.7.3 on all systems

OrthoMCL/2.0.9 now creates its goodProteins.fasta Blast database of orthologs with the -parse_seqids option, so that blastdbcmd queries against this database can extract specific sequences.

pyGenomeTracks (visualisation tools for genome tracks) 2.1 is now installed as module pyGenomeTrakcs/2.1 on all systems.

HiC-Pro (An optimized and flexible pipeline for Hi-C data processing) version 2.11.1 was installed as module HiC-Pro/2.11.1 on all systems

Kourami (A graph-guided assembler for HLA haplotypes covering typing exons (exons 2 and 3 for Class I and exon 3 for Class II) using high-coverage whole genome sequencing data) version 0.9.6 was installed on all systems.

MIP (Mutation Identification Pipeline) version 6.0.0 was installed as module mip/6.0.0 on all systems

The Stampy short read aligner version 1.0.32 is now installed as module Stampy/1.0.32 on all systems.

Mothur (open-source, expandable software to fill the bioinformatics needs of the microbial ecology community) version 1.41.0 is now installed as module Mothur/1.41.0 on all systems.

The Kraken2 sequence classificiation system version 2.0.7-beta as of the commit tagged bc14b13 has been installed as Kraken2/2.0.7-beta-bc14b13 on all systems.  The default database, as well as the special greengenes, rdp and silva databases have been built and will be rebuilt monthly.  See 'module help Kraken2/2.0.7-beta-bc14b13' for more.

Gnu Parallel version 20180822 has been installed on all systems as module gnuparallel/20180822.

InterProScan (scans protein and nucleic acid sequences against InterPro protein signatures, which are predictive models provided by several different databases that make up the InterPro consortium) version 5.30-69.0 is now installed as module InterProScan/5.30-69.0 on all Uppmax systems.

This installation includes support for Panther database 12.0, and the additional analysis tools Phobius/1.01, SignalP/4.1f, and tmhmm/2.0c.

Phobius (combined transmembrane topology and signal peptide predictor) 1.01 has been installed as module Phobius/1.01 on all Uppmax systems.  The 64-bit executable is used for the subsidiary tool decodeanhmm. 

UMI-tools (tools for handling Unique Molecular Identifiers in NGS data sets) versions 0.5.3 and 0.5.4 are now installed as modules umi_tools/0.5.3 and umi_tools/0.5.4 on all systems.

Samstat (sequence statistics) has been installed as module samstat/1.5.1 on all systems.  This module requires samtools, and the samtools/1.8 module will be loaded if another module version of samtools is not already loaded.

Mothur, a bioinformatics package developed by and for the microbial ecology community, has been installed on Rackham, Bianca, and Irma. Versions up to 1.38.1 were previously installed on Milou. Load the module with "module load Mothur/1.40.5".

GenomeThreader (robust de novo gene discovery) version 1.7.0 is now installed as module GenomeThreader/1.7.0 on all systems.

Clustal Omega (large multiple sequence alignments) version 1.2.4 has been installed as module clustalo/1.2.4 on all systems.

MAFFT multiple sequence alignment version 7.407 is now installed on all systems as module MAFFT/7.407.  This includes MAFFT extensions.

The R_packages omnibus module containing R packages has been updated with modules R2jags, rjags, units, and others.  R_packages/3.5.0 contains 11746 CRAN packages, out of 12772 available, and 14544 BioConductor packages, out of 15615 available. See the R_packages module guide for a complete list of available R packages.

JAGS (Just Another Gibbs Sampler) version 4.3.0 is now installed as module JAGS/4.3.0 on all systems.

The UDUNITS library (arithmetic manipulation of units and for conversion of numeric values between compatible units) version 2.2.26 is now installed as module UDUNITS/2.2.26 on all systems.  This module should be loaded before loading the package 'units' from R_packages/3.5.0.

Centrifuge (classifier for metagenomic sequences) has been installed as Centrifuge/1.0.4-beta on all systems.  The indices p_compressed p_compressed+h+v p+h+v p+v v are prebuilt and available in $CENTRIFUGE_DB, set to the appropriate location when the module is loaded.

deepTools (tools for exploring deep sequencing data) version 3.1.0 is now installed as module deepTools/3.1.0 on all systems.

The GATK/3.8-0 module now includes the gatk wrapper script modified from Bioconda, so that GATK can be run from the command line using gatk ... or GenomeAnalysisTK ... directly.

The SRA Toolkit (interaction with NCBI's SRA databases) version 2.9.1-1 is now installed as module sratools/2.9.1-1 on all Uppmax systems.  This includes the fasterq-dump tool to speed the download of FastQ files from SRA.

CIRCexplorer (CIRCexplorer is a combined strategy to identify junction reads from back spliced exons and intron lariats.) version 1.1.10 is now installed as module CIRCexplorer/1.1.10 on all systems.

rvtests (a flexible software package for genetic association analysis for sequence datasets) version 2.0.6 is installed as module rvtests/2.0.6 on all systems.