Parallel assembler for short read sequence data

General purpose finite element modeling package

JAVA build tool

C++ API and toolkit for analyzing and managing BAM files

Utilities for comparing, summarizing and intersecting genomic features in the UCSC Genome Browser BED format

Basic Linear Algebra Subprograms

Search tool that finds regions of local similarity between nucleotide or protein sequences

Peer reviewed C++ source libraries

Ultrafast, memory-efficient tool for aligning sequencing reads to long reference sequences.

Fast light-weight tool that aligns relatively short sequences to a sequence database

Fork of the Celera Assembler designed for high-noise single-molecule sequencing

Programming language designed for productive parallel computing at scale

Tool to control the compilation process. "cmake" comes with the operating system, but it is an old version 2.  Likely you should "module load cmake" which will get you a much newer release of version 3.

Parallel computing platform and API model for Nvidia GPU's

Assembles transcripts, estimates their abundances, tests for differential expression and regulation in RNA-Seq samples

Alignment tool for aligning short DNA sequencing reads to a protein reference database

Generic tool for sequence comparison

Quality control tool for high throughput sequence data

Command line tools for Short-Reads FASTA/FASTQ files preprocessing

Electronic structure program. Licensed for general use

Generates two- and three-dimensional plots of functions

Molecular dynamics software primarily designed for biomolecular systems

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers

Data model, library, and file format for storing and managing data (built with GCC and Intel)

Biosequence analysis using profile hidden Markov models

Interactive Data Language, is a programming language used for data analysis, particularly in astronomy. Special case: restricted to licensed users

High-level, high-performance dynamic programming language for technical computing

Classical molecular dynamics code

Multiple sequence alignment program

Portable and easily configurable genome annotation pipeline

High-level language and interactive environment, performs computationally intensive tasks

Freely available, portable implementation of MPI. Renamed to MPICH

Library exploiting novel features and mechanisms of high-performance networking technologies

Software libraries and self-describing, machine-independent data formats supporting the creation, access, and sharing of array-oriented scientific data

A new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing.
Works with HISAT2 and SRAToolkit

A massively parallel simulator for individual-based modelling of microbial communities

High performance message passing library

Accurate inference of orthogroups, orthologues, gene trees and rooted species

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

Practical Alignment using Sate and TrAnsitivity. This is installed to python/2.
module load python/2. Then pip list will display available modules 

Whole genome association analysis toolset

Quantitative Insights Into Microbial Ecology. Qiime2 is a package in Python3

Language and environment for statistical computing and graphs

A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences

"Rigorous Investigation of Networks Generated using Simulations" is a scientific code developed in Fortran90/MPI to analyze the results of molecular dynamics simulations

A dynamic, reflective, object-oriented, general-purpose programming language.

SAMRAI

Utilities for manipulating alignments in SAM format

Software suite developed by SAS Institute for advanced analytics, multivariate analyses, business intelligence, data management, and predictive analytics.

St. Petersburg genome assembler, for both standard isolates and single-cell MDA bacteria assemblies

An extremely memory-efficient hash_map implementation

Software pipeline for building loci from short-read sequences

Fast splice junction mapper for RNA-Seq reads

Telomere Restriction Fragment (TRF) Analysis

Package which enables the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data

Annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes

Atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. Special case: restricted to licensed users

Tool providing easily accessible methods for working with complex genetic variation data in the form of VCF files

De novo genomic assembler specially designed for short read sequencing technologies

A software library used for data compression.