3D Caffe library for 3D classification or segmentation problem.

1.0.0-rc3

module load caffe-3d

ABAQUS Finite Element Analysis products.

6.14-1, 2016

module load abaqus/2016 or module load abaqus/6.14-1

Mass screening of contigs for antibiotic resistance genes.

0.3, 0.5, 0.7, 0.8

module load abricate/xxx (where xxx is the version)

De novo genome sequence assembler.

1.9.0

module load abyss/1.9.0

De novo genome sequence assembler.

1.9.0, 2.0.2

module load abyss-mpi/1.9.0

This program searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal.

2.2.2

module load adapterremoval/2.2.2

AFNI (Analysis of Functional NeuroImages)

17.2.02

module load afni

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data.

0.9.6

module load afterqc/0.9.6

A code searching tool similar to ack, with a focus on speed.

2.1.0

module load ag/2.1.0

Algorithm for secondary de novo genome assembly guided by closely related references.

3242011

module load aligngraph/3242011

AlleleSeq pipeline - ake a large collection of reads generated from ChIP-seq or RNA-seq experiments associated with an individual and detect single nucleotide variants

1.2a

module load alleleseq/1.2a

The new short read genome assembler from the Computational Research and Development group at the Broad Institute.

52488

module load allpathslg/52488

A collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation.

3.1.0

module load amos/3.1.0

A high-throughput analysis pipeline to identify and characterize resistance genes from metagenomic sequence data

0.0.0

module load amrplusplus

This is the Python 3.5.3 version of Anaconda. Anaconda is the leading open data science platform powered by Python.

4.2.0

module load anaconda/4.2.0

This is the Python 2.7 version of Anaconda. Anaconda is the leading open data science platform powered by Python.

5.0.1, 2019.03

module load anaconda2/

xxx (where xxx is the version)

ANN is a library written in C++, which supports data structures and algorithms for both exact and approximate nearest neighbor searching in arbitrarily high dimensions.

1.1.2

module load ann/1.1.2

Annotation and Ranking of Human Structural Variations

2.1

module load annotsv

Annotation and Ranking of Human Structural Variations

2.1

module load annotsv

A software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).

20150619, 20170716, 20180416

module load annovar/xxx (wheree xxx is the version)

An engineering simulation for general purpose finite element analysis and computational fluid dynamics.

172, 180, 181, 182, 190, 191, 192, 193, 194, 2019R1, 2019R2

module load ansys/xxx (where xxx is the version number)

A unified platform for electromagnetic, circuit and system simulation.

170, 181, 182, 193

module load ansysEM/xxx (where xxx is the version number)

A Java library and command-line tool that builds files as targets and extension points dependent upon each other.

1.9.4, 1.10.3

module load ant/xxx (where xxx is the version)

ANTs computes high-dimensional mappings to capture the statistics of brain structure and function.

2.2.0

module load ants

tRNA (and tmRNA) detection.

1.2.36

module load aragorn/1.2.36

An ANSI C library for parsing GNU style command line arguments

13

module load argtable2

A fast download utility.

1.25.0

module load aria2/1.25.0

Armadillo is a high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use

8.500.0

module load armadillo/8.500.0

Multiresolution domain calling software for chromosome conformation capture interaction matricies.

2.2

module load armatus

None

3.1.5

module load arpack-ng/3.1.5

A genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.

17

module load artemis

ArtificialFastqGenerator takes the reference genome (in FASTA format) as input and outputs artificial FASTQ files in the Sanger format

19_05_2015

module load artfastgen

Automatic Segmentation of Hippocampal Subfields (ASHS)

20170223

module load ashs

Automatically Tuned Linear Algebra Software.

3.10.2, 3.10.3

module load atlas/3.10.2 or module load atlas 3.10.3

A gene prediction program for eukaryotes written by Mario Stanke, Oliver Keller, Stefanie Knig and Lizzy Gerischer. It can be used as an ab initio program, which means it bases its prediction purely on the sequence.

3.2.1, 3.3

module load augustus/3.2.1 or module load augustus/3.3

An extensible package of M4 macros that produce shell scripts to automatically configure software source code packages.

2.69

module load autoconf/2.69

A tool for automatically generating Makefile.in files compliant with the GNU Coding Standards. Automake requires the use of Autoconf.

1.14, 1.15

module load automake/1.14 or module load automake/1.15

count DNA sequence reads in BAM files

0.8.0

module load bam-readcount

This package contains mainly a lightweight C implementation of the read name collation code from the larger libmaus

0.0.50

module load bambamc/0.0.50

BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files.

2.4.0

module load bamtools/2.4.0

Programs for working on SAM/BAM files.

1.0.14

module load bamutil/1.0.14

Bayesian Analysis of Population Structure.

6

module load baps/6

Barrnap predicts the location of ribosomal RNA genes in genomes.

0.6

module load barrnap

A fast and accurate de novo genome assembler for longer NGS reads

1.0

module load base/1.0

BaseSpace Sequence Hub Command Line Interface

0.8.1, 0.9.11.631, 0.10.8

module load basespace/0.8.1 or module load basespace/0.9.11.631

Improved mapper for bisulfite sequencing reads on DNA methylation

1.04b

module load

batmeth/1.04b

BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes

3.0.4

module load bayesass

Bazel is a tool that automates software builds and tests.

0.2.3, 0.3.2, 0.4.3, 0.4.5, 0.5.1, 0.7.0, 0.11.0, 0.16.1, 0.21.0, 0.25.2, 0.28.0

module load bazel/xxx (where xxx represents the version number)

BBMap is a splice-aware global aligner for DNA and RNA sequencing reads.

36.92, 37.98

module load bbmap/36.92 or module load bbmap/37.98

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.

1.1-intel, 1.2, 1.3.1, 1.3.1-intel, 1.5, 1.5-intel, 1.6, 1.6-intel, 1.8, 1.9, 1.9-102

module load bcftools/xxx (where xxx represents the version number)

bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.

2.19

module load bcl2fastq2

Required for supernova

A general purpose library for evaluating the likelihood of sequence evolution on trees.

20150401

module load beagle/20150401

Bayesian Evolutionary Analysis by Sampling Trees.

1.8.2, 2.2.0, 2.3.1, 2.4.2

module load beast/xxx (where xxx represents the version number)

BEDOPS high-performance genomic feature operations

2.4.30

module load bedops/2.4.30

The bedtools utilities are a swiss-army knife of tools for a wide range of genomics arithmetic and analysis tasks.

2.24.0, 2.25.0, 2.26.0

module load bedtools/xxx (where xxx represents the version number)

GNU Binary file utilities.

2.26, 2.30

module load binutils/2.26 or module load binutils/2.30

Tools for early stage alignment file processing

2.0.72

module load biobambam2

Biogeme is an open source freeware designed for the maximum likelihood estimation of parametric models in general, with a special emphasis on discrete choice models.

2.5

module load biogeme/2.26

Biopieces is a bioinformatic framework of tools easily used and easily created.

1

module load biopieces/1

A tool to map bisulfite converted sequence reads and determine cytosine methylation states.

0.18.2, 0.19.0, 0.20.0, 0.22.1

module load bismark/xxx (where xxx is the version)

None

3

module load bison/3

None

3.5.0

module load blas/3.5.0

The PacBio long read aligner

1.3.1

module load blasr/1.3.1

NCBI Basic Local Alignment Search Tool for DNA sequences.

2.2.26, 2.2.30

module load blast/2.2.26 or module load blast/2.2.30

BLAST+ is a suite of command-line tools to run BLAST.

2.3.0, 2.4.0, 2.6.0, 2.7.1

module load blast+/xxx (where xxx is the version number)

Web tools to help understand the human genome.

3.6

module load blat/3.6

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

1.0

module load blobtools

Boost is a set of libraries for the C++ programming language that provide support for tasks and structures such as linear algebra, pseudorandom number generation, multithreading, image processing, regular expressions, and unit testing.

1.55.0, 1.57.0, 1.59.0, 1.61.0, 1.62.0, 1.64.0, 1.66.0, 1.67.0

module load boost/xxx (where xxx represents version number)

Bowtieis an ultrafast, memory-efficient short read aligner.

1.1.1, 1.1.2

module load bowtie/1.1.1 or module load bowtie/1.1.2

Bowtieis an ultrafast, memory-efficient short read aligner.

2.2.5, 2.3.3.1

module load bowtie2/2.2.5 or module load bowtie2/2.3.3.1

Bayesian analysis of genomic sequence data under the multispecies coalescent model.

3.3a

module load bpp/3.3a

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

1.0.0

module load bracken/1.0.0

BRAKER1: Unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS

1.9

module load braker1

Unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS

2, 2.0.6

module load braker2/2.0 or module load braker2/2.0.6

BRIG can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.

0.95

module load brig/0.95

BUSCO completeness assessment employs sets of Benchmarking Universal Single-Copy Orthologs from OrthoDB (www.orthodb.org) to provide quantitative measures of the completeness of genome assemblies, annotated gene sets, and transcriptomes in terms of expected gene content.

1.1b, 2.0, 3.0, 3.0.2

module load busco/xxx (where xxx is the version number)

Bam and Variant Analysis Tools.

1.6

module load bvatools/1.6

BWA is a software package for mapping low divergent sequences against a large reference genome, such as the human genome.

0.6.1, 0.7.12, 0.7.15, 0.7.15-intel, 0.7.16a, 0.7.17

module load bwa/xxx (where xxx represents the version number)

None

1.0.6

module load bzip2/1.0.6

Convert3D Medical Image Processing Tool

1.0.0

module load c3d

Software for Computational Analysis of gene Family Evolution

5

module load cafexp

Caffe is a deep learning framework.

1.0.0-rc3, 1.0.0

module load caffe/1.0.0-rc3 or module load caffe/1.0.0

A New Lightweight, Modular, and Scalable Deep Learning Framework

0.8.1

module load caffe2

None

1.12.18, 1.14.10

module load cairo/1.12.18 or module load cairo/1.14.10

cairomm is a C++ wrapper for the cairo graphics library

1.15.3

module load cairomm

Camino is an open-source software toolkit for diffusion MRI processing.

a844005b39c2fc7fd5d33c6af977e44248de42cd

module load camino

A single molecule sequence assembler for genomes large and small.

1.3, 1.6, 1.7, 1.8, 1.8+268

module load canu/xxx (where xxx is the version number)

CAP3 Sequence Assembly Program.

20150421

module load cap3/20150421

None

3.5.0

module load cblas/3.5.0

Microbiome classification pipeline

0.1,

1.

1.

3

module load

ccmetagen/xxx (where xxx is the version)

A program for clustering and comparing protein or nucleotide sequences.

4.6.1, 4.6.5

module load cd-hit/4.6.1

The C-library cddlib is a C implementation of the Double Description
Method of Motzkin et al. for generating all vertices (i.e. extreme points)
and extreme rays of a general convex polyhedron

094h

module load cddlib

A set of analysis pipelines that perform sample demultiplexing, barcode processing, and single cell gene counting

3.0.2

module load cellranger

Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labelling of reads and quantification of species.

1.0.3-beta, 1.0.4-beta

module load centrifuge/1.0.3-beta

CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.

3.4.10, 3.41

module load cfitsio/xxx (where xxx is the version)

A collaborative effort to develop a robust, easy to use, and efficient C++ software library of geometric data structures and algorithms.

4.5.1, 4.7, 4.9, 4.10, 4.11

module load cgal/xxx (where xxx is the version)

The CFD General Notation System (CGNS) provides a general, portable, and extensible standard for the storage and retrieval of computational fluid dynamics (CFD) analysis data.

3.2.1

module load cgns/3.2.1

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data.

1.11

module load chimera/1.11

ChimeraSlayer is a chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp).

20110519

module load chimeraslayer/20110519

ChunkChromosome is a helper utility for minimac and MaCH.

27-05-14

module load chunkchromosome

Flexible and automatable circular data visualisation.

0.69-3

module load circos/0.69-3

A Class Library for High Energy Physics.

2.1.1.0, 2.2.0.8, 2.3.1.1

module load clhep/xxx (where xxx represents the version number)

Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data

0.9

module load

clinsv/0.9

Efficient inference of recombination in bacterial genomes.

1

module load clonalframeml/1

Multiple alignment of nucleic acid and protein sequences

1.2.4

module load clustal-omega

Multiple alignment of nucleic acid and protein sequences

2.1

module load clustal

Cross-platform, open-source build system.

3.0.1, 3.4.0, 3.9.4, 3.11.4, 3.13.4

module load cmake/xxx (where xxx represents the version number)

A tool for CNV discovery and genotyping from depth-of-coverage by mapped reads

0.4

module load cnvnator

codonPhyML uses Markovian codon models of evolution in phylogeny reconstruction.

dev_1.00_201407.24, 20150402

module load codonphyml/dev_1.00_201407.24 or module load codonphyml/20150402

Correlated evolution of substitution rates and quantitative traits

1.5

module load coevol/1.5

CONN is a Matlab-based cross-platform software for the computation, display, and analysis of functional connectivity in fMRI (fcMRI).

15g, 17a

module load conn/15g or module load conn/17a

An efficient and low-memory software framework for analysis of genomes using sequence data.

1.0.5.21

module load cortex/1.0.5.21

CREST (Clipping Reveals Structure) is a new algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data.

0.01

module load crest/0.01

CUDA is NVIDIA's parallel computing architecture.

6.0.37, 6.5.14-test, 6.5.14, 7.5.18, 8.0.44, 9.0.176, 9.1.85, 9.2.148, 10.0.130, 10.1.105

module load cuda/xxx (where xxx represents version number)

CUDA is NVIDIA's parallel computing architecture.

6.0.37, 6.5.14-test,6.5.14, 7.5.18

module load cuda2/6.0.37

Transcriptome assembly and differential expression analysis for RNA-Seq.

2.2.1

module load cufflinks/2.2.1

curl is used in command lines or scripts to transfer data.

7.59.0

module load curl/7.59.0

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

1.8.3

module load cutadapt/1.8.3

Cyberduck CLI program "duck"

0.6.2

module load cyberduck/0.6.2. Can upload directly to AARNet CloudStor from Artemis HPC. Use a CloudStor App password instead of your UniKey Password.

None

1.8.16

module load dbus/1.8.16

None

0.104

module load dbus-glib/0.104

dcm2niix is a designed to convert neuroimaging data from the DICOM format to the NIfTI format.

1.0.20170624

module load dcm2niix

DCMTK is a collection of libraries and applications implementing large parts the DICOM standard.

3.6.1

module load dcmtk/3.6.1

Delly is an integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data.

0.6.7, 0.7.6, 0.7.8, 0.7.9

module load delly/xxx (where xxx is the version)

DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation

1.11