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Owens

Early Access Period

Owens is expected to be available to all OSC clients on a later date to be announced. A small number of projects will be given access during the preceding 5 weeks to help us with testing and to provide feedback. Early access is by application only; the application deadline has passed.

Early access will be granted in several stages beginning August 15, 2016. Applicants will receive notification of their access date via ServiceNow.

Oakley, Owens

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:

Oakley, Owens

STAR: Spliced Transcripts Alignment to a Reference.

Availability and Restrictions

The following versions of STAR are available on OSC clusters:

Oakley, Owens

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.

Oakley, Owens

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:

Oakley, Owens

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:

Oakley, Owens

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:

Oakley, Owens

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.

Availability and Restrictions

The following versions of Trimmomatic are available on OSC clusters:

Oakley, Owens

bam2fastq is used to extract raw sequences (with qualities) from programs like SAMtools, Picard, and Bamtools.

Availability and Restrictions

The following versions of bam2fastq are available on OSC clusters:

Oakley, Owens

GMAP: a genomic mapping and alignment program for mRNA and EST sequences.

Availability and Restrictions

The following versions of GMAP are available on OSC clusters:

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