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Oakley, Owens

SAM format is a generic format for storing large nucleotide sequence alignments. SAMtools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

Availability and Restrictions

The following versions of SAMtools are available on OSC clusters:

Oakley, Owens

GATK is a software package for analysis of high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance.

Availability and Restrictions

The following versions of GATK are available on OSC clusters:

BWA

Oakley, Owens

BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM.

Availability and Restrictions

The following versions of BWA are available on OSC clusters:

Oakley, Owens

Bowtie1 is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

Availability and Restrictions

The following versions of Bowtie1 are available on OSC clusters:

Oakley, Owens

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. While each individual tool is designed to do a relatively simple task, quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

Oakley

NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.

Availability and Restrictions

The following versions of NWChem are available on OSC clusters:

Owens

To cite Owens, please use the following Archival Resource Key:

ark:/19495/hpc6h5b1

Here is the citation in BibTeX format:

@article{Owens2016,
ark = {ark:/19495/hpc93fc8},
url = {http://osc.edu/ark:/19495/hpc6h5b1},
year  = {2016},
author = {Ohio Supercomputer Center},
title = {Owens supercomputer}
}

And in EndNote format:

Oakley

ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.

Oakley, Owens

"Condo model" refers to an arrangment when a client leases one or more compute nodes for the shared cluster while OSC provides all infrastructure, as well as maintenance and services. BMI's Condo on the Oakley Cluster is leased by the Biomedical Informatics Institute at The Ohio State University. This condo is a temporary "bridge" condo to server the community needs until the Owens Cluster is available.

Hardware

Detailed system specifications for the Oakley condo:

Glenn, Oakley, Owens, Ruby

Introduction

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