Bioinformatics & Biology

Bismark

Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step.

Availability and Restrictions

Versions

The following versions of bedtools are available on OSC clusters:

Clustal W

Clustal W is a multiple sequence alignment program written in C++.

Availability and Restrictions

Versions

The following versions of bedtools are available on OSC clusters:

MUSCLE

MUSCLE is a program for creating multiple alignments of protein sequences.

Availability and Restrictions

Versions

The following versions of bedtools are available on OSC clusters:

metilene

metilene is a software tool to annotate differentally methylated regions and differentially methylated CpG sites.

Availability and Restrictions

Versions

The following versions of bedtools are available on OSC clusters:

Desmond

Desmond is a software package that perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters, general-purpose supercomputers, and GPUs. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms containing a large number of processors, but may also be executed on a single computer.

Software Refresh - August/September 2018

OSC is refreshing the software stack for Owens and Ruby on September 4, 2018. This will be done by a rolling reboot. During the software refresh, some default versions are updated to be more up-to-date. Information about the old and new default versions, as well as all available versions of each software package will be included on the corresponding OSC software webpage. See https://www.osc.edu/supercomputing/software-list.

BLAST Database

 

OSC periodically updates The NCBI BLAST database. 

Versions

BLAST database is available on the Owens and Oakley clusters. The versions currently available at OSC are:

VERSION OWENS PITZER

2017-03

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