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.

The RNA-seq pseudoalignment tool kallisto version 0.43.1 has been installed on all systems as module kallisto/0.43.1.

An updated version of cufflinks has been installed as module cufflinks/2.2.1-b55bb21 on all systems.  This contains a fix for an unusual case in which extremely long runtimes have been observed; more information is available here.

The R packages Lahman, RJSONIO, ecodist, gee, hflights, igraph, optparse, proto, and reshape and the BioConductor packages ROC, TCC, baySeq, multtest, and phyloseq, together with their dependencies, have been added to the R_packages/3.4.0 module.  For a complete list of packages available, see the R_packages user guide.

The most recent version of Picard tools has been installed as module picard/2.10.3 on all systems.

The modules samtools/1.5, htslib/1.5, and bcftools/1.5 have been installed on all systems.  Note that the most recent versions of the tabix and bgzip tools are now found in the htslib module, and not the tabix module.

Bismark 0.18.2 has been installed as module bismark/0.18.2 on all systems.  The earlier bismark module versions 0.14.5, 0.15.0, 0.16.1 and 0.16.2 are also installed on rackham; they were previously available on milou, bianca and irma.

vsearch 2.4.3 has been installed as module vsearch/2.4.3 on all systems.

RTG Tools 3.8.1 (utilities for accurate VCF comparison and manipulation) has been installed as module rtgtools/3.8.1 on all systems.

MAGeCK 0.5.6 (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) is now installed as module MAGeCK/0.5.6 on all systems.

MrBayes (Bayesian inference and model choice) is now installed on Rackham as module mrbayes/3.2.6. 

Beagle-lib (general purpose library for evaluating the likelihood of sequence evolution on trees) is now installed on Rackham as module beagle/2.1.2. 

MultiQC 1.0 (aggregates results from bioinformatics analyses across many samples into a single report) is now installed as module MultiQC/1.0 on all systems.

deepTools 2.5.1 is now installed as module deepTools/2.5.1 on all systems.

deepTools 2.4.3 has been installed as module deepTools/2.4.3 on all systems.

The seqtk tool version 1.2-r101 has been installed on all systems as module seqtk/1.2-r101.  The earlier version 1.0-r57 has also been installed on all systems as module seqtk/1.0-r57, and the module versions seqtk/1.0-r31 and seqtk/1.0-r68e, previously available only on milou, have been installed on rackham, irma and bianca.

TEtools 1.0.0 up through commit 283c1ca has been installed as module TEtools/1.0.0-283c1ca on all systems.  The local UPPMAX version has been modified to move some options provided only in config files to command-line options.

The omnibus module perl_modules/5.24.1 has been installed on all systems.  This module contains many commonly-used and not-so-commonly used perl modules, for use with the perl/5.24.1 module, which is also loaded.  Note that perl/5.24.1 uses 64-bit integers and pointers.  See the linked page for a list of the contents of this omnibus module.

Perl6 Rakudo Star 2017.04 has been installed as module perl6/rakudo-star-2017.04 on all systems.  This module also modifies the environment for development against MoarVM if so desired.

The editor emacs has been installed as module emacs/25.2 on all systems.  Emacs is already installed on all systems but this module provides the most recent version.

GIFLIB (library providing GIF support via libgif) is now installed as module libgif/5.1.4 on all systems.

The ATLAS tool for working with ancient DNA has been installed as module ATLAS_aDNA/20170510 on all systems.  Note the module name is ATLAS_aDNA, because the name ATLAS has already being given to a module for the widely used numeric library.

The Armadillo C++ linear algebra library has been installed as module Armadillo/7.900.0 on all systems.

MethylDackel 0.2.1 (renamed continuation of methylation detection tool PileOMeth) is now installed as module MethylDackel/0.2.1 on all systems.

Perl 5.24.1 (the most recent stable distribution) has been installed as perl/5.24.1 on all systems.  Perl modules perl/5.22.2 and perl/5.24.0, previously available only on milou, are now also available on rackham, irma and bianca.   All perl modules with versions 5.24+ are built with 64-bit integers and pointers.

The scripting language m4  and the build tool libtool are now installed as modules m4/1.4.17 and libtool/2.4.6 on all systems.

MALDER has been installed as module malder/1.0 on milou.

p7zip (Linux port of popular 7zip archiver from Windows) 16.02 is now installed as module p7zip/16.02 on all systems.  The executable file is named 7za.

ProtExcluder 1.1 (scripts to remove fragmented proteins during repeat library construction) is installed as module ProtExcluder/1.1 on all systems.

miRDeep2 (miRNA discovery) version 2.0.0.8 is now installed as module mirdeep2/2.0.0.8 on all systems.

The most recent version of MetaSV (accurate and integrative structural-variant caller for next generation sequencing) has now been installed as module MetaSV/0.5.4 on all systems.

The latest SPAdes assembler is now installed as spades/3.10.1 on all systems.  Earlier versions 3.6.0, 3.8.0, 3.8.1, 3.9.0 and 3.10.0 are also now available on rackham, irma and bianca.

AGE (sequence alignment in the presence of structural variants) 0.4 is installed as module AGE/0.4 on all systems.  The executable age_align is built without parallel support, while the executable age_align_omp is built with parallel support.  See 'module help AGE/0.4' for more information.

eLSA (extended local similarity analysis) has been installed as module eLSA/20160907-febe2d7a57c8 on all systems.

GEMINI (comprehensive genome variant annotation) 0.20.0 has been installed as module GEMINI/0.20.0 on all systems.  The earlier versions GEMINI/0.18.3 and GEMINI/0.20.0 have also been extended to rackham, irma and bianca.  As before, the additional CADD and GERP annotation datasets have been included.

The most recent version of the fermikit assembly-based variant calling pipeline is now installed as module fermikit/0.14-prerelease-96f7820 on all systems.  The previously installed fermikit/r178 is now also available on rackham, irma and bianca.

The latest SpeedSeq (rapid genome analysis and interpretation) is installed as module SpeedSeq/0.1.2-20170504-30f8dc6 on all systems.  The module version reflects the most recent release, as well as the date and commit of the repository clone for this installed module.  See 'module help SpeedSeq/0.1.2-20170504-30f8dc6' for more information on available data.

CNVnator 0.3.3 (copy-number variant detection) has been installed as module CNVnator/0.3.3 on all systems.

ROOT 6.06.08 (data analysis framework from CERN) has been installed as ROOT/6.06.08 on all systems.

Cairo 1.14.8 (device-independent graphics rendering library) has been installed as module cairo/1.14.8 on all systems.

Poppler 0.54.0 (library for rendering PDF) has been installed as module Poppler/0.54.0 on all systems.

Salmon 0.8.2 is now installed as module Salmon/0.8.2 on all systems.

LEON-BIS (identify conserved areas in protein alignments) is now installed as module LEON-BIS/20130322 on all systems.  See 'module help LEON-BIS/20130322' for more information.

ATLAS (Automatically Tuned Linear Algebra Software) library version 3.10.3 is now installed on all systems. It was previously available only on milou. It has been tuned separately for milou, rackham and irma, and the bianca version is linked to the rackham build.

MethPipe 3.4.3 (computational pipeline for analyzing bisulfite sequencing data) is now installed as module MethPipe/3.4.3 on all systems.

The standard RAxML has been updated to version 8.2.10 both with and without MPI support on all systems.  The modules are raxml/8.2.10-gcc and raxml/8.2.10-gcc-mpi.

RAxML-NG (reimplementation of RAxML) 0.2.0b is installed on all systems.  The default module ins installed as RAxML-NG/0.2.0b, and the module enabled for MPI is installed as RAxML-NG/0.2.0b-mpi.

CEGMA 2.5 (tool for assessing assembly completeness) is now installed as cegma/2.5 on all systems.

BUSCO 2.0.1 has been installed as module BUSCO/2.0.1 on all systems.  There is an extensive list of BUSCO lineage sets available, see the module help.  BUSCO/1.22 has also been installed on rackham, irma and bianca.

Several versions of the bowtie and bowtie2 modules have been made available on rackham, irma and bianca.  Available are bowtie/0.12.9, bowtie/1.1.2, bowtie2/2.1.0, bowtie2/2.2.9.

samtools 1.4 and htslib 1.4 have been installed as samtools/1.4 and htslib/1.4 on all systems.

samblaster 0.1.22 and 0.1.24 have been installed on all systems as modules samblaster/0.1.22 and samblaster/0.1.24.  Previously, only samblaster/0.1.22 was available, and only on milou.

SeqMonk 1.37.1 is now installed as module seqmonk/1.37.1 on all systems.

MAKER 2.31.9 has been installed on all systems as module maker/2.31.9.  This module also uses updated versions of several external modules (RepeatMasker/4.0.7, augustus/3.2.3, snap/2013-11-29, blast/2.4.0+, openmpi/2.1.0 [if used]) and adds GeneMark/4.32-es as a de novo gene finder.

SignalP 4.1c has been installed on rackham, irma and bianca.  This version was previously available on milou, and given the version number 4.1.  On all systems, this module can be loaded with SignalP/4.1c.

tRNAscan-SE 1.3.1 has been installed on rackham, irma and bianca as module tRNAscan-SE/1.3.1.

GNU binutils 2.28 is now installed as module binutils/2.28 on all systems.

The augustus gene discovery tool version 3.2.3 is now installed on milou, rackham, irma and bianca.  This is an update for milou and a new installation for the other systems.

SNAP (gene prediction tool) version 2013-11-29 is now installed as module snap/2013-11-29 on all systems.

USEARCH 9.2.64 (32-bit version) has been installed on all systems as module usearch/9.2.64.  All previously installed versions are also now available on all systems.

Delly (structural variant discovery) 0.7.6 is installed on all systems as delly/0.7.6.  The additional tools delly-suave and delly-maze have not been installed.

The last pairwise sequence aligner version 847 is now installed as module last/847 on all systems.

vcflib (VCF file filtering) is now updated on milou and installed on all other systems as vcflib/2017-04-04.

Gnu awk 4.1.4 is now installed as module gawk/4.1.4 on all systems.

Two UPPMAX-local database copies have been updated: ExAC to version 0.3.1 and CDD to version 3.16. 

The Pfam protein family database version 31.0 is now installed locally on Uppmax.  The pfam_scan module is updated to pfam_scan/1.6 to handle new formats in the new Pfam release.

Variant Effects Predictor version 87 is now installed as module vep/87 on all systems.  Locally-cached databases and plugins are also available.  Note that this version still uses the script from the Ensembl package (varient_effects_predictor.pl) rather than the new script from the now-separate, beta version (vep).

IGV 3.0-beta (Integrated Genome Viewer with support for long reads) is now installed as module IGV/3.0-beta on all systems.

IGV (Integrated Genome Viewer) 2.3.92 and IGVtools 2.3.91 are now installed as modules IGV/2.3.92 and IGVtools/2.3.91, respectively, on all systems.

Jellyfish (flexible kmer counter) 2.2.6 is now installed as module jellyfish/2.2.6 on milou, rackham, irma and bianca.

Haskell Tool Stack 1.4.0 is installed as module haskell-stack/1.4.0 on milou and rackham.

Texlive 2016 is now installed as module texlive/2016 on milou and rackham.

The UCSC 'Kent' utilities version 345 are now installed as module ucsc-utilities/v345 on milou.

Redundans (pipeline that assists assembly of heterozygous/polymorphic genomes) 0.13a-20170321 (version 9.13a with commits up to today) is now installed on milou and rackham.

RepeatModeler 1.0.8_RM4.0.7 is now installed on milou and rackham.  This is the existing RepeatModeler 1.0.8, configured to use the newer RepeatMasker/4.0.7 and updated versions of the auxiliary tools.

RepeatMasker 4.0.7 is now installed on Milou and Rackham.  This module version also contains updated rmblastn and trf tools and provides nhmmer and cross_match as additional search tools.

HDF5 (high-performance data file format) 1.8.18 is now installed on milou and rackham.  SZIP is supported via the szip/2.1.1 module and GZIP is supported via the gzip/1.2.11 module. On both clusters there are two module versions available.  hdf5/1.8.18 is compiled with the system GCC compiler, and hdf5/1.8.18_gcc6.3.0 is compiled with the gcc/6.3.0 module.

freetype (open-source type rendering library) 2.7.1 is now installed on milou and rackham.

szip (high-performance compression library) 2.1.1 is now installed on milou and rackham.

zlib (general compression library) 1.2.11 is installed on milou and rackham.  zlib/1.2.8 remains the default module version on milou.

Ragout (chromosome assembly using multiple references) 2.0-20170312 is now installed as module Ragout/2.0-20170312 on milou and rackham.

SiBELia (synteny exploration tool) 3.0.6 is now installed as module SiBELia/3.0.6 on milou and rackham.

AdmixTools tools (admixture in human populations) version 5.0-20170312 is now installed on milou as module AdmisTools/5.0-20170312.

IQ-TREE 1.5.3 (phylogenomic software by maximum likelihood) is installed as module iqtree/1.5.3-omp as part of the phylogeny subgroup of bioinfo-tools on milou and rackham.  The multicore executable is available as iqtree-omp and the single core executable as iqtree.

Meerkat 0.189 (detection of somatic structural variants) has been installed as module Meerkat/0.189 on milou.

Primer3 2.3.7 (package for designing PCR primers) is now installed as module Primer3/2.3.7 on milou.