Software

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:

eXpress

eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.

Availability and Restrictions

The following versions of eXpress are available on OSC clusters:

Ncview

Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc.

Availability and Restrictions

Versions

The following versions of Ncview are available on OSC clusters:

Subread

The Subread package comprises a suite of software programs for processing next-gen sequencing read data like Subread, Subjunc, featureCounts, and exactSNP.

Availability and Restrictions

The following versions of Subread are available on OSC clusters:

VCFtools

VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.

Availability and Restrictions

The following versions of VCFtools are available on OSC clusters:

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