Software

STAR-Fusion

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

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

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:

Trimmomatic

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:

bam2fastq

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:

GMAP

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:

FASTX-Toolkit

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

Availability and Restrictions

The following versions of FASTX-Toolkit are available on OSC clusters:

SnpEff

SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes).

Availability and Restrictions

The following versions of SnpEff are available on OSC clusters:

SRA Toolkit

The Sequence Read Archive (SRA) stores raw sequence data from "next-generation" sequencing technologies including 454, IonTorrent, Illumina, SOLiD, Helicos and Complete Genomics. In addition to raw sequence data, SRA now stores alignment information in the form of read placements on a reference sequence. Use SRA Toolkit tools to directly operate on SRA runs.

Availability and Restrictions

The following versions of SRA Toolkit are available on OSC clusters:

RNA-SeQC

RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files. The output consists of HTML reports and tab delimited files of metrics data. This program can be valuable for comparing sequencing quality across different samples or experiments to evaluate different experimental parameters. It can also be run on individual samples as a means of quality control before continuing with downstream analysis.

Availability and Restrictions

The following versions of RNA-SeQC are available on OSC clusters:

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