None

3.1.5

module load arpack-ng/3.1.5

ART is a set of simulation tools to generate synthetic next-generation sequencing reads.

2.6.0

module load art

None

3.5.0

module load cblas/3.5.0

Microbiome classification pipeline

0.1

module load ccmetagen

Flexible and automatable circular data visualisation.

0.69-3

module load circos/0.69-3

CIRI (circRNA identifier) is a novel chiastic clipping signal based algorithm

2.0

module load ciri-full

codonPhyML uses Markovian codon models of evolution in phylogeny reconstruction.

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

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.

Molecular electronic structure program

2018.1

module load dalton

None

2.25_v1.01, 2.16_2.17_v1.01, py3

module load epimine/xxx (where xxx represents

Eval is a flexible tool for analyzing the performance of gene-structure prediction programs.

2.2.8

module load eval

Comprehensive, accurate and fast distance-based phylogeny inference program

2.1.5

module load fastme

The FastML server is a bioinformatics tool for the reconstruction of ancestral sequences based on the phylogenetic relations between homologous sequences.

3.1, 3.1-b

module load fastml/3.1 or module load fastml/3.1-b

fqtools is a software suite for fast processing of FASTQ files.

2.1

module load fqtools/2.1

FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes.

1.31

module load fraggenescan

The GDC Data Transfer Tool provides an optimised method of transferring data to and from the GDC, and enables resumption of interrupted transfers.

1.2.0, 1.4.0

module load gdc-client/1.2.0xxx (where xxx is the version)

GenomeMasker (gmasker) masks over-represented words in the FASTA file, preventing design of primers in repeated regions.

1.3

module load genomemasker

GenomeThreader is a software tool to compute gene structure predictions

1.7.1

module load genomethreader

A version control system for software development and other version control tasks.

2.14.1, 2.16.2

module load git/2.14.1 or module load git/2.16.2

Git extension for versioning large files

2.7.1

module load git-lfs

gperftools is a collection of a high-performance multi-threaded malloc() implementation, plus some pretty nifty performance analysis tools.

2.5

module load gperftools/2.5

A robust tool for the prediction of multiple lipid modification sites

1

module load gps-lipid

HLAscan is an alignment-based program that determines haplotypes taking read distribution into account.

4

module load hlascan

Various utility tools for working with genomics data

4.5

module load hmftools

Software for identifying recombination hotspots from population SNP data.

1.2.1-modified

module load hotspotter

HPC GridRunner is a simple command-line interface to high throughput computing using a variety of different grid computing platforms

1.0.2

module load hpcgridrunner

iCommands is a collection of commands for Linux and Mac OS operating systems that are used in the iRODS system to interact with the CyVerse Data Store.

4.1.10

module load icommands

Intel MPI libraries.

15.1, 18.1

module load intel-mpi/15.1 or module load intel-mpi/18.1

Protein sequence analysis and classification

5.28-67.0,5.34-73.0

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

This program takes paired end Illumina short read sequence data, an IS query of interest and a reference genome or assembly and reports the locations of the IS query in the reference genome or the assembly.

0.1.3

module load is_mapper/0.1.3

ISOWN: Identification of SOmatic mutations Without Normal tissues

1.0

module load isown

KMC K-mer Counter is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects.

2.1.1

module load kmc/2.1.1

Identification of GPI-anchor signals by a Kohonen Self Organizing Map

1.5

module load kohgpi

The second version of the Kraken taxonomic sequence classification system. Kraken is a system for assigning taxonomic labels to short DNA sequences

1, 2.0.6-beta, 2.0.7-beta

module load kraken2/xxx (where xxx is the version number)

Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.

2.7

module load kronatools

Linkage disequilibrium applying Malecot-Morton model to genetic data

LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values.

1.14, 1.16

module load ldmap

LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values.

1.14, 1.16

module load leveldb/1.leveldb/1.14 or module load leveldb/1.16

Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.

1.3.0

module load magicblast

MakeHub is a command line tool for the fully automatic generation of of track data hubs1 for visualizing genomes with the UCSC genome browser

i

module load makehub

Mayavi 3D scientific data visualization and plotting in Python

MaxBin clusters metagenomic contigs into different bins, each consists of contigs from one species.

2.2.6

module load mayavimaxbin2

Mayavi 3D scientific data visualization and plotting in Python

4.5

module load mayavi

The MCL algorithm is short for the Markov Cluster Algorithm.

14-137

module load mcl/14-137

Matlab compiler runtimes

R2013a, R2014a, R2014b, R2016a, R2016b, R2017a

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

Mercurial is a free, distributed source control management tool.

3.8.3

module load mercurial/3.8.3

MetaBAT: A robust statistical framework for reconstructing genomes from metagenomic data

2.12.1

module load metabat

A Sequencing Simulator for Genomics and Metagenomics.

0.9.5

module load metasim

Meta-analysis for multi-tissue eQTL studies.

0.4

module load metatissue/0.4

An extension of Velvet assembler to de novo metagenomic assembly

1.2.02

module load metavelvet

Programs and Scripts for Bisulphite Sequence Data

2017

module load methprogs

A deep learning framework.

0.7.0, 1.0.0, 1.4.0

module load mxnet/0.7.0 or module load mxnet/1.0.0xxx (where xxx is the version)

Pipeline to generate complete public health microbiology reports from sequenced isolates.

1.01, 1.20, 1.41, 2.0, 2.0.20181010.b9b2d41

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

Open Source High-Performance Computational Chemistry

6.8.1

module load nwchemxxx is the version)

Open source implementation of the MPI-2 message passing protocol for parallel computations. Compiled with PGI compilers.

1.8.4

module load openmpi-pgi/1.8.4

OpenSlide is a C library that provides a simple interface to read whole-slide images

3.4.1

module load openslide

OpenSSL is an open source project that provides a robust, commercial-grade, and full-featured toolkit for the Transport Layer Security (TLS) and Secure Sockets Layer (SSL) protocols. It is also a general-purpose cryptography library.

1.0.1s, 1.0.1t, 1.1.0h.1s, 1.0.1t, 1.1.0h

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

An Ab Initio, DFT and Semiempirical electronic structure package

4.1.1

module load orca/4.1.1

Identifying missing annotations for evolutionarily conserved genes.

1.1.1

module load openssl/xxx (where xxx is the version number)orthofiller

An Ab Initio, DFT and Semiempirical electronic structure package

Accurate inference of orthologs, orthogroups, the rooted species, gene trees and gene duplcation events tree

2.2.7

module load orca/4.1.2orthofinder

ParaView is an open-source, multi-platform data analysis and visualization application.

4.0.1, 4.4.0, 5.4.1, 5.6.0

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

A program to align short sequences

2.31

module load pass

Pheniqs is a generic high throughput DNA sequence demultiplexer and quality analyzer written in multi threaded C++11.

1.1.1

module load pheniqs/1.1.1

A hidden Markov Model capable of predicting both Transmembrane Topology and Signal peptides

1.01

module load phobius

A tool for creating 3D graphics.

3.6.1

module load povray/3.6.1

Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment.

v1.1.alpha19

module load pplacer

PReprocessing and INformation of SEQuence data.

0.20.4

module load prinseq/0.20.4

A series of python scripts to process data generated using the 10x genomics DNA system.

0.0.2

module load proc10x

This software package infers population size history from a diploid sequence using the Pairwise Sequentially Markovian Coalescent (PSMC) model.

0.6.5-r67Markovian Coalescent (PSMC) model.

0.6.5-r67

module load psmc/0.6.5-r67

Light-weight, simple and fast XML parser for C++

1.9

module load psmc/0.6.5-r67pugixml

QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.

py2.7.9, py2.7.10

module load qiime/py2.7.9, module load qiime/py2.7.10

Identify quantitative trait loci (QTL) and Marker Simulator

1.1

module load qmsim

QUAST evaluates genome assemblies. For metagenomes, please see MetaQUAST project.

3.2, 4.3, 5.0.2

module load quast/3.2 or module load quast/4.3xxx (where xxx is the version)

None

2.2.2, 2.5.1

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

Rapid Alignment-free Quantification of Isoform Abundance

0.10.0

module load sailfish)

Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.

0.8.2, 0.11.0, 0.12.0, 0.13.1

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

SDL_image is an image file loading library.

1.2.12

module load sdl_image/1.2.12

SecretomeP 1.0 produces ab initio predictions of non-classical i.e. not signal peptide triggered protein secretion in eukaryotes.

1.0

module load secretomep

STAR RNA-seq aligner

2.4.0j, 2.5.2a, 2.6.1b, 2.7.0e

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

StrainPhlAn is a tool for strain-level resolution of species across large sample sets, based on single nucleotide polymorphisms (SNPs) within conserved and unique species marker genes

5.2.2

2.4.0j, 2.5.2a, 2.6.1b

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

A set of programs for the taxonomic analysis of nucleotide sequence data

1.13.3

module load targetptaxator-tk

Library of basic elements ('widgits') for building a graphical user interface. It is typically used with Tcl.

8.6.3

module load tk/8.6.3

Transmembrane helices in proteins

2.0c

module load tmhmm

The approximate regex matching library and agrep command line tool.

0.8.0

module load tre

A tool for automated alignment trimming in large-scale phylogenetic analyses.

1.4.1

module load trimaltre

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data.

030816, 0.6.1

Nonemodule load trimgalore/xxx (where xxx is the version)

A tool for automated alignment trimming in large-scale phylogenetic analyses.

1.4.1

module load trimal

The Visualization Toolkit is an open-source, freely available software system for 3D computer graphics, image processing, and visualization.

5.0.0, 5.8.0, 6.3.0, 7.1.1, 8.2.0

run "module avail vtk" on Artemis to see available versionsmodule load vtk/5.0.0 or module load vtk/7.1.1

WCSLIB 5.16 - an implementation of the FITS WCS standard.

5.16

module load wcslib

Weka is a collection of machine learning algorithms for data mining tasks. (in java)

3.8.3

module load weka