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.

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'.

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.

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.

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.

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.

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.

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.

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

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.

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.

PLINK (A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Future development will revolve around critical extensions to the core file format (multiallelic variants, dosage, phase). version 2.00-c1defe4 installed on all systems as module plink/2.00-c1defe4

KrakenHLL (taxonomic sequence classification system with unique k-mer counting) version 0.4.9 has been installed as module KrakenHLL/0.4.9 on all systems.

Blobtools (A modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets) version 1.0 is now installed as module blobtools/1.0 on all UPPMAX systems.

MALDER (admixture estimation) version 1.0 is now available as module malder/1.0 on all UPPMAX systems.  It was previously available only on milou.

BBMap package version 38.08 is now installed as module bbmap/38.08 on all UPPMAX systems.

LDhelmet (statistical inference for fine-scale variable recombination rate estimation) version 1.10 is now installed as module LDhelmet/1.10 on all UPPMAX clusters.

IQ-Tree (phylogenetic tree construction) version 1.6.5 is now installed as module iqtree/1.6.5-omp-mpi on all systems.  Different executables provide single-core, multi-core single-node, MPI, and hybrid MPI solutions.  See 'module help iqtree/1.6.5-omp-mpi' for more information.

Cutadapt (read trimming) version 1.16 has been installed as module cutadapt/1.16 on all UPPMAX systems.  This version uses a python 3 virtual environment and supports threading.

Ensembl Variant Effect Predictor version 92.3 is now installed as module vep/92 on all systems. Cache files, fasta files and plugins are also installed. See the module help for information.

SnpEff (variant annotation) version 4.3t is installed as module snpEff/4.3t on all systems.  This installation also includes the databases CanFam3.1.75, CanFam3.1.86, GRCh37.75, GRCh37.p13.RefSeq, GRCh38.86, GRCh38.p7.RefSeq.

KAT (Kmer Analysis Toolkit) 2.4.2 is now installed as module KAT/2.4.2 on all systems.

PBSuite (PacBio assembler) version 15.8.24 is now installed as module PBSuite/15.8.24 on all systems.  It was previously installed only on milou.

The R_packages omnibus package 3.5.0 is now installed on all systems as packages R_packages/3.5.0.  This package includes 11937 CRAN packages installed, out of 12571 available, and 14735 BioConductor packages installed, out of 15411 available.

R (statistical system) version 3.5.0 is now installed as module R/3.5.0 on all systems.

New version of htslib (1.8) installed as module htslib/1.8

CD-HIT (sequence clustering) version 4.6.8-2017-1208 has been installed as module cd-hit/4.6.8-2017-1208 on all systems.

FastTree (fast phylogenetic tree inference) version 2.1.10 has been installed as module FastTree/2.1.10 on all systems.  Three executables are available, including single- and multi-threaded versions; see 'module help FastTree/2.1.10' for more information.

Eigensoft 7.2.1 (with the fix restoring the ploteig tool) is now installed as module eigensoft/7.2.1 on all systems.

AdmixTools version 5.0 with the latest commit as of 2017 Oct 24, which includes the qpDpart and rolloffp tools, is now installed as module  AdmixTools/5.0-20171024 on all systems.  Also installed on all systems are AdmixTools/20160803 and AdmixTools/5.0-20170312, previously available only on milou.

BUSCO (Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs) version 3.0.2b is now installed on all systems as module BUSCO/3.0.2b.

Ruby 2.5.0 is now installed as module ruby/2.5.0 on all systems.

ANGSD (program for analysing next generation sequencing data) 0.921 is now installed as module ANGSD/0.921 on all systems.

fastPHASE (estimate missing genotypes and unobserved haplotypes) 1.4.8 is now installed on all systems as fastPHASE/1.4.8, and fastPHASE/1.4.0 is now available on all systems.  It was previously available only on milou.

Gubbins (rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences) version 2.3.1 is now installed as module gubbins/2.3.1 on all systems.

MultiQC (aggregate results from bioinformatics analyses across many samples into a single report) version 1.5 is now installed as module MultiQC/1.5 on all systems.

gvcftools (utilities to analyse gVCF files) versions 0.16.2 and 0.17.0 are now available on all systems as modules gvcftools/0.16.2 and gvcftools/0.17.0.  These were previously available on just milou.

Stacks (RAD-Seq assembly and variant calling) versions 1.48 and 2.0Beta9 are now installed as modules Stacks/1.48 and Stacks/2.0Beta9 on all systems.

Canu (assembler for long noisy read data) version 1.7 has been installed as module canu/1.7 on all systems.

ImageMagick (image manipulation) version 6.9.9-35 has been installed as module ImageMagick-6.9.9-35 on all systems.  In addition to the ImageMagick executables, this module provides libraries and include files for building against ImageMagick (e.g., for the R package 'magick').  The module also includes an installation of libwebp 0.6.1 which includes the cwebp/dwebp executables.

Salmon (RNA-seq transcript quantification) version 0.9.1 is now installed as module Salmon/0.9.1 on all systems.

mergeSVcallers (Software for merging different Tabix merged VCF files) is now installed as module mergeSVcallers/161006-23533ef on all systems.

Gmap and gsnap (genomic alignment programs) version 2018-02-12 have been installed as module gmap-gsnap/2018-02-12 on all systems.  As per the developer's website, versions 2018-mm-dd and later do not yet have support for mapping to genomes >~4Gbp via the programs gmapl and gsnapl.  For large genome support, load an earlier module version such as gmap-gsnap/2017-09-11.

RStudio version 1.1.423 is installed on rackham, irma and bianca.  This precompiled version cannot be installed on milou.

Canu (assembler for long noisy reads) version 1.6 is now installed as module canu/1.6 on all systems.  For this version and all canu module versions >= 1.1, the global default for the useGrid option is set to be useGrid=false, to avoid problems with Canu's attempts to use SLURM to manage assembly jobs.  This can be overridden via configuration files or command-line options.

Artemis (genome browser from Wellcome Sanger Institute) version 16.0.0 is now installed as module artemis/16.0.0 on all systems.

PhyloPhlAn (computational pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information) version 0.99 is now installed as module phylophlan/0.99 on all systems.

CheckM (tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes) version 1.0.11 is now installed as module CheckM/1.0.11 on all systems.

MEGAHIT (large and complex metagenomics assembly via succinct de Bruijn graph) 1.1.2 is now installed as megahit/1.1.2 on all systems.  The installed version is CPU-only, as GPUs are not available at UPPMAX.

BEAST (Bayesian analysis of phylogenies using MCMC, independent from BEAST2) version 1.8.4 is installed on all systems except for milou as module beast/1.8.4.

BEAST2 (Bayesian evolutionary analysis by sample trees) version 2.4.8 is installed on all systems as module beast2/2.4.8.  This module automatically loads the BEAGLE library module beagle/2.1.2.

LUMPY (general probabilistic framework for structural variant discovery) version 0.2.13-213a417, which is the 0.2.13 release updated to the most recent commit, is installed as module LUMPY/0.2.13-213a417 on all systems.

The 10X Chromium assembler Supernova version 2.0.0 has been installed as module supernova/2.0.0 on all systems.  The previous module versions supernova/{1.0.0,1.1.1,1.1.4} are also now available on all systems.

The Illumina base caller bcl2fastq version 2.20.0 is now installed as module bcl2fastq/2.20.0 on all systems.