Owens cluster will be decommissioned on February 3, 2025. Some pages may still reference Owens after Owens is decommissioned , and we are in the process of gradually updating the content. Thank you for your patience during this transition
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 is a graph-based alignment program that maps DNA and RNA sequencing reads to a population of human genomes.
FreeSurfer is a software package used to anaylze nueroimaging data.
The following versions of FreeSurfer are available on OSC clusters:
FSL is a library of tools for analyzing FMRI, MRI and DTI brain imaging data.
The following versions of FSL are available on OSC clusters:
OSC is refreshing the software stack for Oakley and Ruby on February 22, 2017 (during the scheduled downtime). During the software refresh, some default versions are updated to be more up-to-date and some older versions are removed. 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.
Bowtie2 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. Bowtie 2 supports gapped, local, and paired-end alignment modes.
BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
The following versions of BamTools are available on OSC clusters:
STAR: Spliced Transcripts Alignment to a Reference.
The following versions of STAR are available on OSC clusters:
Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.
The following versions of Trimmomatic are available on OSC clusters:
bam2fastq is used to extract raw sequences (with qualities) from programs like SAMtools, Picard, and Bamtools.
The following versions of bam2fastq are available on OSC clusters:
