Annotation and Ranking of Human Structural Variations

2.1

module load annotsv

Annotation and Ranking of Human Structural Variations

2.1

module load annotsv

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)

Convert3D Medical Image Processing Tool

1.0.0

module load c3d

Software for Computational Analysis of gene Family Evolution

5

module load cafexp

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

3.0.2

module load cellranger

Efficient inference of recombination in bacterial genomes.

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

The DNAnexus Platform SDK

0.276.0

module load dx-toolkit

A cross-platform C++ GUI toolkit

0.9

module load clinsv/0.9

GNU AWK later version

5.0.0

module load gawk

Gblocks is a computer program written in ANSI C language that eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences.

0.91b

module load gblocks/0.91b

GNU Multiple Precision Arithmetic Library.

4.3.2, 5.1.3, 6.1.0, 6.1.2

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

GTFtools provides a set of functions to analyze various modes of gene models

0.6.5

module load gtftools

Image Processing and Analysis Cross platform image library

1.8.0

module load il

Image Processing and Analysis in Java.

148

module load imagej/148

KMA is a mapping method designed to map raw reads directly against redundant databases

1.1.4, 1.2.10a, 1.2.4

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

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, 2.7.1

module load kronatools

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

20150210, 20163007kSNP does SNP discovery and SNP annotation from whole genomes

3.1

module load ksnp/3.1

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

20150210, 20163007-test, 20163007, 20161711, 20172601, 20181603

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

LASTZ is a program for aligning DNA sequences, a pairwise aligner.

1.03.73, 1.04

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

NoneOpenFabrics Interfaces (OFI) is a framework focused on exporting fabric communication services to applications. Libfabric is a core component of OFI

31.27.1

module load libffi/3.2.1libfabric

None

3.2.1

module load libffi/3.2.1

FreeImage is an Open Source library project for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications.

3.18.0

module load libfreeimage/3.18.0

C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result.

0.8.1,1.0.3, 1.1.0

module load mpc/0.8.1 or module load mpc/1.0.3xxx (where xxx is the version)

C library for multiple-precision floating-point computations with correct rounding.

2.4.2, 3.1.4, 4.0.2

module load mpfr/2.4.2 or module load mpfr/3.1.4

OpenBLAS ODE is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.open source, high performance library for simulating rigid body dynamics

0.2.14, 0.2.18, 0.3.416

module load openblas/xxx (where xxx is the version)ode

OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library.A scalable tool for rapid detection of selective sweeps in whole-genome datasets

2.4.11, 3.4.02.5

module load opencvomegaplus/2.4.11 2.5

OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.

0.2.14, 0.2.18, 0.3.4

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

OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library.

2.4.11, 3.4.0

module load opencv/2.4.11 or module load opencv/3.4.0

NonePneumococcal Capsular Typing tool for NGS data

01.31.03

module load popplerpneumocat/01.31.03

None

0.31.0

module load poppler/0.31.0

A tool for creating 3D graphics.

3.6.1

module load povray/3.6.1

A cross-platform and ultrafast toolkit for FASTA

1.10.1

module load seqkit

A container application for reproducible research computing

3.2.1

module load singularity/3.2.1

Short Linear Motif discovery and analysis

1.8.1

module load slimsuite/1.8.1

SMALT aligns DNA sequencing reads with genomic reference sequences.

0.7.6

module load smalt/0.7.6

Bayesian genotyper for structural variants.

0.0.2

module load svtyper/0.0.2

Likelihood-based Selective Sweep Detection

3.2.4

module load sweed/3.2.4

A program written in C that can perform genomic scans for recent selective sweeps selection while controlling for background selection and mutation rate variation.

1

module load sweepfinder2/1

None

3.0.5

module load swig/3.0.5

A synteny-aware orthologue clusering tool

1.1

module load synerclust/1.1

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

0.2.6

module load tabix/0.2.6

tantan is a tool to mask simple regions (low complexity and short-period tandem repeats) in DNA, RNA, and protein sequences.

22

module load tantan