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Ascend, Cardinal, Owens, Pitzer
Linaro HPC tools analyze how HPC software runs. It consists of three applications, Linaro DDT, Linaro Performance Reports and Linaro MAP:
Owens, Pitzer
Sometimes the best way to get access to a piece of software on the HPC systems is to install it yourself as a "local install". This document will walk you through the OSC-recommended procedure for maintaining local installs in your home directory or project space. The majority of this document describes the process of "manually" building and installing your software.
Owens, Pitzer
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:
Owens, Pitzer
STAR: Spliced Transcripts Alignment to a Reference.
Availability and Restrictions
Versions
The following versions of STAR are available on OSC clusters:
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.
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
Versions
The following versions of STAR-Fusion are available on OSC clusters:
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.
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
Versions
The following versions of MIRA are available on OSC clusters:
Owens, Pitzer
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
Versions
The following versions of Trimmomatic are available on OSC clusters:
