Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB.
Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command-line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. It may also be used as a batch-oriented language.
Octave has extensive tools for solving common numerical linear algebra problems, finding the roots of nonlinear equations, integrating ordinary functions, manipulating polynomials, and integrating ordinary differential and differential-algebraic equations. It is easily extensible and customizable via user-defined functions written in Octave's own language, or using dynamically loaded modules written in C++, C, Fortran, or other languages.
While our python installations come with many popular packages installed, you may come upon a case where you need an addiditonal package that is not installed. If the specific package you are looking for is available from Anaconda.org (formerlly binstar.org) you can easily install it and required dependencies by using the Conda package manager.
To be able to install a package using the conda package manager:
While we provide a number of Python modules, you may need a module we do not provide. If it is a commonly used module, or one that is particularly difficult to compile, you can contact OSC Help for assistance, but we have provided an example below showing how to build and install your own Python modules, and make them available inside of Python.
OSC provides Allinea Performance Reports and Allinea MAP to all OSC users.
- Allinea Performance Reports: very simple tool to generate one single-page HTML report that presents overall performance characteristics of HPC applications
- Allinea MAP: HPC application profiler with easy-to-use GUI environment.
The following versions of Allinea are available on OSC clusters:
Sometimes the best way to get access to a piece of software on the HPC systems is to install it yourself as a "local install". This document will walk you through the OSC-recommended procedure for maintaining local installs in your home directory or project space.
Early Access Period
Owens is expected to be available to all OSC clients on a later date to be announced. A small number of projects will be given access during the preceding several weeks to help us with testing and to provide feedback. Early access is by application only; the application deadline has passed.
Early access will be granted in several stages beginning August 22, 2016. Applicants will receive notification of their access date via ServiceNow.
BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
Availability and Restrictions
The following versions of BamTools are available on OSC clusters:
STAR: Spliced Transcripts Alignment to a Reference.
Availability and Restrictions
The following versions of STAR are available on OSC clusters:
miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs. The tool reports known and hundreds of novel microRNAs with high accuracy in seven species representing the major animal clades. The low consumption of time and memory combined with user-friendly interactive graphic output makes miRDeep2 accessible for straightforward application in current reasearch.