Bioinformatics & Biology

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.

TopHat

TopHat uses Bowtie, a high-throughput short read aligner, to analyze the mapping results for RNA-Seq reads and identify splice junctions.

 

Please note that tophat (and bowtie) cannot run in parallel, that is, on multiple nodes.  Submitting multi-node jobs will only waste resources.  In addition you must explicitly include the '-p' option to use multiple threads on a single node.

Kallisto

Kallisto is an RNA-seq quantification program. It quantifies abundances of transcripts from RNA-seq data and uses psedoalignment to determine the compatibility of reads with targets, without needing alignment.

FreeSurfer

FreeSurfer is a software package used to anaylze nueroimaging data.

Availability & Restrictions

Versions

The following versions of FreeSurfer are available on OSC clusters:

FSL

FSL is a library of tools for analyzing FMRI, MRI and DTI brain imaging data.

Availability and Restrictions

Versions

The following versions of FSL are available on OSC clusters:

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 https://www.osc.edu/supercomputing/software-list.

Bowtie2

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

BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.

Availability and Restrictions

Versions

The following versions of BamTools are available on OSC clusters:

STAR

STAR: Spliced Transcripts Alignment to a Reference.

Availability and Restrictions

Versions

The following versions of STAR are available on OSC clusters:

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