Bioinformatics & Biology


FreeSurfer is a software package used to anaylze nueroimaging data.

Availability & Restrictions


The following versions of FreeSurfer are available on OSC clusters:


GPU-BLAST is an accelerated version of the popular NCBI-BLAST ( that uses general-purpose graphics processing unit (GPU). In comparison to the sequential NCBI-BLAST, GPU-BLAST is nearly four times faster, while producing identical results.

Availability & Restrictions

GPU-BLAST is available without restriction to all OSC users.

The following versions of GPU-BLAST are available on OSC systems:

Software Refresh - February 2017

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


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. 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.

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.

Availability and Restrictions

The following versions of miRDeep2 are available on OSC clusters:


STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.

Availability and Restrictions

The following versions of STAR-Fusion are available on OSC clusters:


HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis. It is a collection of command line programs for unix-style operating systems written in mostly perl and c++. Homer was primarily written as a de novo motif discovery algorithm that is well suited for finding 8-12 bp motifs in large scale genomics data.

Availability and Restrictions

The following versions of HOMER are available on OSC clusters:


MIRA - Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and IonTorrent data. PacBio: CCS and error corrected data usable, uncorrected not yet.

Availability and Restrictions

The following versions of MIRA are available on OSC clusters:


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