Bioinformatics & Biology

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 OAKLEY

2017-03

X*

TrimGalore

TrimGalore is a wrapper tool that automates quality and adapter trimming to FastQ files. It also provides functionality to RRBS sequence files.

FastQC

FastQC provides quality control checks of high throughput sequence data that identify areas of the data that may cause problems during further analysis.

Cufflinks

Cufflinks is a program that analyzes RNA -Seq samples. It assembles aligned RNA-Seq reads into a set of transcripts, then inspects the transcripts to estimate abundances and test for differential expression and regulation in the RNA-Seq reads.

HISAT2

HISAT2 is a graph-based alignment program that maps DNA and RNA sequencing reads to a population of human genomes.

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