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:
Owens
STAR
STAR: Spliced Transcripts Alignment to a Reference.
Availability and Restrictions
Versions
The following versions of STAR are available on OSC clusters:
miRDeep2
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
Versions
The following versions of miRDeep2 are available on OSC clusters:
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
Versions
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
Versions
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
Versions
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
Versions
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
Versions
The following versions of bam2fastq are available on OSC clusters:
GMAP
GMAP is a genomic mapping and alignment program for mRNA and EST sequences.
Availability and Restrictions
Versions
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
Verisons
The following versions of FASTX-Toolkit are available on OSC clusters:
