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.

Snakemake (A workflow management tool to create reproducible and scalable data analyses) version 4.5.0 is now installed as module snakemake/4.5.0 on all systems.

SPAdes assembler version 3.11.1 is now installed as module spades/3.11.1 on all systems.

CONSEL (Program for assessing the confidence of phylogenetic tree selection) is now installed as module CONSEL/0.2.0 on all systems.

PLINK/SEQ (A library for the analysis of genetic variation data; a toolset for working with human genetic variation data) version 0.10 is now installed as module plinkseq/0.10 on all systems.

ATSAS (program suite for small-angle scattering data analysis from biological macromolecules) 2.8.3-1 is now installed as module ATSAS/2.8.3-1 on all systems.

BEDTools (a powerful toolset for genome arithmetic) version 2.27.1 is now installed as module BEDTools/2.27.1 on all systems.

svprops (Computes various SV statistics from an input Delly VCF file) version 20171020-ebf6762 is now installed as module svprops/20171020-ebf6762 on all systems. See 'module help svprops/20171020-ebf6762' for details on running this.

Strelka2 (germline and somatic small variant caller) version 2.8.4 is now installed as module Strelka2/2.8.4 on all systems.

The Beta 5 version of GATK 4 has been installed on all systems as module GATK/4.beta.5.  This is used differently from earlier versions of GATK.  See 'module help GATK/4.beta.5' for more information.

pplacer (place reads on a phylogenetic tree) version 1.1.alpha19 has been installed as module pplacer/1.1.alpha19 on all systems.

Freebayes 1.1.0 (variant calling) has been installed on all systems as module freebayes/1.1.0.

R 3.4.3 together with the omnibus package module R_packages 3.4.3 have been installed on all systems as modules R/3.4.3 and R_packages/3.4.3, respectively.  See the link for R_packages to see which packages are included.

MEGAN (interactive microbiome analysis tool) 6.10.5 Academic Edition is installed as module MEGAN/6.10.5 on all systems.

Cramtools 3.0 is installed as module cramtools/3.0 on all systems.

MariaDB (open-source fork of MySQL) versions 10.1.29 and 10.2.11 have been installed as modules MariaDB/10.1.29 and MariaDB/10.2.11 on all systems.  Uppmax does not allow persistent database servers beyond the extent of a single job; we recommend using sqlite for serverless SQL databases of convenience.  These modules may also be useful for compiling software expecting to use a MySQL client to access remote databases.

Bowtie2 2.3.3.1 has been installed as module bowtie2/2.3.3.1 on all systems.

VIM 8.0-1360 (version 8.0 through patch level 1360) has been installed as module vim/8.0-1360 on all systems.  This installation includes support for python, python3, perl and tcl interpreters.  See 'module help vim/8.0-1360 for more information.

SMRT Link v5.0.1 (PacBio software suite) is now installed as module SMRT/5.0.1 on all systems.  This apparently includes all tools previously included in the SMRT Analysis set of tools.

Blasr 5.3.f72428d (PacBio long-read aligner) has been installed as module blasr/5.3-20171117-f72428d on all systems.

PySam version 0.13 has been installed on all systems as module pysam/0.13-python2.7.11 (for python/2.7.11) and pysam/0.13-python3.6.0 (for python/3.6.0).

NCBI taxonomy databases are now available as local copies at Uppmax.  See our NCBI taxonomy databases page for more information.

NCBI UniVec and UniVec_Core databases have been added to the local copies of Blast databases available at **/sw/data/uppnex/blast_databases/**.  As with other local copies of Blast databases, when one of the **blast** modules is loaded these databases are available by specifying '**-db UniVec**' or '**-db UniVec_Core**'.  See our Blast databases page for more information.

PRANK (probabilistic multiple alignment) 170427 is now installed as module prank/170427 on all systems.

Minimap2 (versatile sequence alignment program, good for noisy long reads) 2.4 is installed as module minimap2/2.4 on all systems.

BWA 0.7.17 is installed as module bwa/0.7.17 on all systems.

Trim Galore! 0.4.4 has been installed as module TrimGalore/0.4.4 on all systems.

Nextflow 0.26.0 has been installed as module Nextflow/0.26.0 on all systems.

Preseq 2.0 has been installed as module preseq/2.0 on all systems.

Cutadapt 1.14 has been installed as module cutadapt/1.14 on all systems.

Kraken (system for assigning taxonomic labels to short DNA sequences) 1.0 has been installed as module Kraken/1.0 on all systems.

After a long lull, the local copies of Blast databases are now being updated.  Some additional databases have been added, and the WGS database (not updated locally since 2014) is no longer available.  See the resource page for local Blast databases for more information.

Vsearch (open-source alternative to usearch) 2.5.2 has been installed as module vsearch/2.5.2 on all systems.

Several packages have been added and many have been updated in the module R_packages/3.4.0.  See http://www.uppmax.uu.se/support/user-guides/r_packages-module-guide/ for a complete list of the available packages.

The SRA Toolkit version 2.8.2-1 has been installed as module sratools/2.8.2-1 on all systems.  The SRA Toolkit provides access to SRA datasets as well as special Blast+ tools that enable searching against the WGS and TSA sequence databases.

PLINK 1.90b4.9 (beta version as of 13 Oct 2017) is now available as module plink/1.90b4.9 on all systems.  The previously available module plink/1.90 has been renamed plink/1.90b3n, to reflect its being an earlier beta version (11 May 2015).

NextGenMap version 0.5.4 has been installed as module NextGenMap/0.5.4 as part of bioinfo-tools on all systems.

Pilon (automated genome assembly improvement and variant detection tool) version 1.22 is now installed as module Pilon/1.22 on all systems.

REAPR (tool that evaluates the accuracy of a genome assembly using mapped paired end reads) 1.0.18 has been installed as module REAPR/1.0.18 on all systems.

SeqTools (three sequence alignment visualisation tools from the Sanger Institute) 4.44.1 is now installed as module SeqTools/4.44.1 on all systems.

ShoRAH (short reads assembly into haplotypes) 1.1.0 is now installed as module ShoRAH/1.1.0 on all systems.

The IGV genome viewer version 2.4.2 and associated IGVtools 2.3.98 have been installed as modules IGV/2.4.2 and IGVtools/2.3.98 on all systems.  The module IGV/3.0-beta is removed, as all of its additional features are now in IGV/2.4.2 and it is no longer available for download.

The modules for the most recent version of the Velvet assembler, velvet/1.2.10 and velvet/1.2.10_K128, now contain multiple velvetg and velveth versions with additional capabilities, including support for long sequences and big assemblies.  See 'module help velvet/1.2.10' and 'module help velvet/1.2.10_K128' for more information.

LDhelmet (fine-scale recombination estimates) version 1.9 is now installed as module LDhelmet/1.9 on all systems.

MetaBat (tool for accurately reconstructing single genomes from complex microbial communities) 2.12.1 has been installed as module MetaBat/2.12.1 on all systems.

ExpansionHunter (look for size differences in human-genome small-repeat regions) 2.5.3 is installed as ExpansionHunter/2.5.3 on all systems.  See 'module help ExpansionHunter/2.5.3' for the location of repeat-specs for several human genome releases.

MAKER (genome annotation pipeline) version 3.01.1-beta has been installed as module maker/3.01.1-beta on all systems.

The RMBlast that is part of the RepeatMasker/4.0.7 module has been repaired.  If you ever had rmblastn segfault with the message: "Critical: (109.4) CObject::RemoveLastReference: CObject was referenced again" while running RepeatMasker, this should correct that problem.

GeneMark-ES (unsupervised gene-finding in eukaryotic genomes) version 4.33 is now installed as module GeneMark/4.33-es on all systems.

Trinotate (transcript annotation) version 3.0.2 is now installed as module trinotate/3.0.2 on all systems.

SignalP (signal peptide prediction) version 4.1f is now installed as module SignalP/4.1f on all systems.  Use is restricted to academic users only.

TransDecoder (identifies candidate coding regions within transcript sequences) 5.0.1 is now installed as module TransDecoder/5.0.1 on all systems.

MultiQC 1.2 (comprehensive reporting for bioinformatics analyses) has been installed as module MultiQC/1.2 on all Uppmax systems.

MaSuRCA 3.2.3 (whole-genome assembler) has been installed as module MaSuRCA/3.2.3 on all systems.

Several more modules have been added to the perl_modules/5.24.1 omnibus module, primarily within Statistics::*.

VarScan (variant detection tool) version 2.4.2 has been installed as module VarScan/2.4.2 on all systems.

GMAP-GSNAP version 2017-09-11 has been installed as module gmap-gsnap/2017-09-11 on all systems.

Chromium Cellranger version 2.0.2 has been installed as module cellranger/2.0.2 on all systems.  The directory structure has also changed slightly for earlier versions of the cellranger module and its associated data; please reload the module for new locations.

ANNOVAR 2017.07.16 (comprehensive variant annotation) has been installed on all systems as module annovar/2017.07.16.  A wide range of annotation databases has also been downloaded, for genome builds hg19 and hg38; see 'module help annovar/2017.07.16' for more information.

BBTools/BBMap (toolkit for read mapping and sequence analysis) has been installed as module bbmap/37.53 on all systems.

AdapterRemoval (adapter removal and read merging) version 2.2.2 has been installed as module AdapterRemoval/2.2.2 on all systems.  In addition, the earlier version AdapterRemoval/2.1.7, previously available only on milou, has also been installed on all systems. 

Vmatch (large-scale sequence analysis software) 2.3.0 has been installed as module Vmatch/2.3.0 on all systems.

BEDOPS (BAM file manipulation) version 2.4.28 has been installed as module BEDOPS/2.4.28 on all systems.

PAML (Phylogenetic Analysis by Maximum Likelihood) 4.9e is installed as module paml/4.9e on all systems.

PhyloBayes version 4.1c has been installed as phylobayes/4.1c on all systems.

PhyloBayes MPI version 1.8 is now installed as module phylobayesmpi/1.8 on all systems. 

GATK Queue version 3.8-0 has been installed as module GATK-Queue/3.8-0 on all systems.

Genome Analysis Toolkit version 3.8-0 is installed on all systems as module GATK/3.8-0.  In addition to other improvements, this version corrects core dumps within the PairHMM library that some users have reported.

The local data caches for vep/84 and vep/86 have been reduced to just homo_sapiens.  The local data caches for vep/87 and vep/89 remain complete.  For more information, see http://www.uppmax.uu.se/resources/databases/other-uppnex-oriented-local-data-resources/ and 'module help vep'.

BioPerl 1.7.1 for Perl 5.24.1 has been installed as module BioPerl/1.7.1_Perl5.24.1 on all systems.

Spaln (space-efficient spliced alignment) version 2.3.1 is now installed as module spaln/2.3.1 on all systems.

Sickle (short read quality-based correction) version 1.33-20-g4b0dc85-mullins, based off a maintained fork of the original source tree, has been installed as module sickle/1.33-20-g4b0dc85-mullins on all systems.

SHORE (mapping and analysis pipeline for short DNA sequences) 0.9.3 is now installed as module SHORE/0.9.3 on all systems.

Sambamba 0.6.6 (SAM/BAM file processing) has been installed as module sambamba/0.6.6 on all systems.

Scalpel (indel detection) 0.5.3 has been installed as module scalpel/0.5.3 on all systems.

MAFFT 7.310 (multiple sequence aligner) is installed as module MAFFT/7.310 on all systems.

Jemalloc 5.0.1 (general purpose malloc implementation) has been installed as module jemalloc/5.0.1 on all systems.  The earlier installed module version jemalloc/3.6.0 is also now available on all systems.

Khmer 2.1.1 (k-mer counting library) is installed as module khmer/2.1.1 on all systems.

NGSadmix version 32 and fastNGSadmix (versioned based on repository date/commit hash) are available as modules NGSadmix/32 and fastNGSadmix/20170825-099ab7f on all systems.

LASTZ 1.04.00 (pairwise sequence aligner) has been installed as module lastz/1.04.00 on all systems.

The non-commercial version of RTG Core version 3.8.3 has been installed as module rtgcore/3.8.3 on all systems.  This includes all functionality of rtgtools/3.8.3 as well as additional commands.

RTG Tools version 3.8.3 has been installed as module rtgtools/3.8.3 on all systems.

FastQ Screen version 0.11.1 has been installed as module fastq_screen/0.11.1 on all systems.

Anfo (short-read mapper for divergent reads) version 0.98 is now available as module anfo/0.98 on all systems.  This module was installed for the now-decommissioned kalkyl but didn't work properly for milou, and this is now corrected for all systems. The earlier module version anfo/0.97 is removed.  This version of the program is quite old (~8 y).

Gnuplot 5.0.7 is installed as module gnuplot/5.0.7 on all systems.

Amazon Web Services Command-Line Interface version 1.11.140 is now installed as module awscli/1.11.140 on all systems.

HTSeq version 0.9.1 has been installed as module htseq/0.9.1 on all systems.

ITSx (detection of ITS regions in ribosomal sequences) versions 1.0.11 and 1.1-beta are now installed on all systems.  Both versions are new installations for all systems; note that 1.1-beta is a beta (preliminary) release.

RSeQC 2.6.4 (RNA-Seq quality control) is now installed as module rseqc/2.6.4 on all systems.

The MaSuRCA assembler version 3.2.2 is now installed as module MaSuRCA/3.2.2 on all systems.

KAT (K-mer Analysis Toolkit) version 2.3.4 has been installed as module KAT/2.3.4 on all systems.

RealTime Genomics' preformatted reference databases are now available on Uppmax systems.  See 'module help rtgtools/3.8.1' for more information.

Pblat-cluster (blat aligner with hybrid parallel support via MPI) version 0.3 has been installed as pblat-cluster/0.3 on all systems.  Note that module pblat/2.0, with single-node multithreading, is also available.

Pblat (threaded version of blat aligner) version 2.0 has been installed as module pblat/2.0 on all systems.

EPACTS 3.3.0-a5209db (version based off of latest bug-fix commit) has been installed as module EPACTS/3.3.0-a5209db on all systems.

MELT (Mobile Element Locator Tool) version 2.0.2 has been installed as module MELT/2.0.2 on all systems.