Bioinformatics & Biology

Bowtie2

Bowtie 2 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

The following versions of BamTools are available on OSC clusters:

STAR

STAR: Spliced Transcripts Alignment to a Reference.

Availability and Restrictions

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

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

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:

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