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

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

2.0

module load ciri-full

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

Predicting fungal effector proteins from secretomes using machine learning

1.0

module load effectorp

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

2.2.8

module load eval

The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures.

v1.1.1

module load evidencemodeler

A collection of fast C routines to compute the discrete Fourier transform.

2.1.5-gcc, 3.3.3-avx, 3.3.3-gcc, 3.3.4-gcc, 3.3.5-intel

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

A set of tools to analyze genomic data with a focus on Next Generation Sequencing.

0.8.0

module load fgbio

A free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary.GenomeThreader is a software tool to compute gene structure predictions

1.57.91

module load genometools/1.5.9genomethreader

A free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary.

1.5.9

module load genometools/1.5.9

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

NoneiCommands 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.

544.1.10

module load icu/54.1icommands

None

54.1

module load icu/54.1

None

1.1.2

module load idba/1.1.2

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

LAST finds similar regions between sequences.

894

module load last/894

Linkage disequilibrium applying Malecot-Morton model to genetic data

2.0

module load ldmap

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

1.3.0.0

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 magicblastmakehub

Open Source High-Performance Computational Chemistry

6.8.1

module load nwchem

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

PRESEQ Software for predicting library complexity and genome coverage in high-throughput sequencing.

2.0

module load preseq

PReprocessing and INformation of SEQuence data.

0.20.4

module load prinseq/0.20.4

PReprocessing and INformation of SEQuence dataA series of python scripts to process data generated using the 10x genomics DNA system.

0.200.42

module load prinseq/0.20.4proc10x

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

None

2.2.2, 2.5.1

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

NoneRapid Alignment-free Quantification of Isoform Abundance

20.2.2, 2.5.110.0

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

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

module load strainphlan

Tabix indexes a TAB-delimited genome position file and creates an index file.

0.2.6index file.

0.2.6

module load tabix/0.2.6

TargetP predicts the subcellular location of eukaryotic protein sequences

1.1

module load tabix/0.2.6targetp

Transmembrane helices in proteins

2.0c

module load tmhmm

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

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